sdk/cwl/arvados_cwl/arvcontainer.py

   1 # Copyright (C) The Arvados Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: Apache-2.0
   4
   5 from future import standard_library
   6 standard_library.install_aliases()
   7 from builtins import str
   8
   9 import logging
  10 import json
  11 import os
  12 import urllib.request, urllib.parse, urllib.error
  13 import time
  14 import datetime
  15 import ciso8601
  16 import uuid
  17 import math
  18
  19 import arvados_cwl.util
  20 import ruamel.yaml as yaml
  21
  22 from cwltool.errors import WorkflowException
  23 from cwltool.process import UnsupportedRequirement, shortname
  24 from cwltool.utils import aslist, adjustFileObjs, adjustDirObjs, visit_class
  25 from cwltool.job import JobBase
  26
  27 import arvados.collection
  28
  29 from .arvdocker import arv_docker_get_image
  30 from . import done
  31 from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location, remove_redundant_fields, make_builder
  32 from .fsaccess import CollectionFetcher
  33 from .pathmapper import NoFollowPathMapper, trim_listing
  34 from .perf import Perf
  35 from ._version import __version__
  36
  37 logger = logging.getLogger('arvados.cwl-runner')
  38 metrics = logging.getLogger('arvados.cwl-runner.metrics')
  39
  40 class ArvadosContainer(JobBase):
  41     """Submit and manage a Crunch container request for executing a CWL CommandLineTool."""
  42
  43     def __init__(self, runner, job_runtime,
  44                  builder,   # type: Builder
  45                  joborder,  # type: Dict[Text, Union[Dict[Text, Any], List, Text]]
  46                  make_path_mapper,  # type: Callable[..., PathMapper]
  47                  requirements,      # type: List[Dict[Text, Text]]
  48                  hints,     # type: List[Dict[Text, Text]]
  49                  name       # type: Text
  50     ):
  51         super(ArvadosContainer, self).__init__(builder, joborder, make_path_mapper, requirements, hints, name)
  52         self.arvrunner = runner
  53         self.job_runtime = job_runtime
  54         self.running = False
  55         self.uuid = None
  56
  57     def update_pipeline_component(self, r):
  58         pass
  59
  60     def _required_env(self):
  61         env = {}
  62         env["HOME"] = self.outdir
  63         env["TMPDIR"] = self.tmpdir
  64         return env
  65
  66     def run(self, toplevelRuntimeContext):
  67         # ArvadosCommandTool subclasses from cwltool.CommandLineTool,
  68         # which calls makeJobRunner() to get a new ArvadosContainer
  69         # object.  The fields that define execution such as
  70         # command_line, environment, etc are set on the
  71         # ArvadosContainer object by CommandLineTool.job() before
  72         # run() is called.
  73
  74         runtimeContext = self.job_runtime
  75
  76         if runtimeContext.submit_request_uuid:
  77             container_request = self.arvrunner.api.container_requests().get(
  78                 uuid=runtimeContext.submit_request_uuid
  79             ).execute(num_retries=self.arvrunner.num_retries)
  80         else:
  81             container_request = {}
  82
  83         container_request["command"] = self.command_line
  84         container_request["name"] = self.name
  85         container_request["output_path"] = self.outdir
  86         container_request["cwd"] = self.outdir
  87         container_request["priority"] = runtimeContext.priority
  88         container_request["state"] = "Committed"
  89         container_request.setdefault("properties", {})
  90
  91         runtime_constraints = {}
  92
  93         if runtimeContext.project_uuid:
  94             container_request["owner_uuid"] = runtimeContext.project_uuid
  95
  96         if self.arvrunner.secret_store.has_secret(self.command_line):
  97             raise WorkflowException("Secret material leaked on command line, only file literals may contain secrets")
  98
  99         if self.arvrunner.secret_store.has_secret(self.environment):
 100             raise WorkflowException("Secret material leaked in environment, only file literals may contain secrets")
 101
 102         resources = self.builder.resources
 103         if resources is not None:
 104             runtime_constraints["vcpus"] = math.ceil(resources.get("cores", 1))
 105             runtime_constraints["ram"] = math.ceil(resources.get("ram") * 2**20)
 106
 107         mounts = {
 108             self.outdir: {
 109                 "kind": "tmp",
 110                 "capacity": math.ceil(resources.get("outdirSize", 0) * 2**20)
 111             },
 112             self.tmpdir: {
 113                 "kind": "tmp",
 114                 "capacity": math.ceil(resources.get("tmpdirSize", 0) * 2**20)
 115             }
 116         }
 117         secret_mounts = {}
 118         scheduling_parameters = {}
 119
 120         rf = [self.pathmapper.mapper(f) for f in self.pathmapper.referenced_files]
 121         rf.sort(key=lambda k: k.resolved)
 122         prevdir = None
 123         for resolved, target, tp, stg in rf:
 124             if not stg:
 125                 continue
 126             if prevdir and target.startswith(prevdir):
 127                 continue
 128             if tp == "Directory":
 129                 targetdir = target
 130             else:
 131                 targetdir = os.path.dirname(target)
 132             sp = resolved.split("/", 1)
 133             pdh = sp[0][5:]   # remove "keep:"
 134             mounts[targetdir] = {
 135                 "kind": "collection",
 136                 "portable_data_hash": pdh
 137             }
 138             if pdh in self.pathmapper.pdh_to_uuid:
 139                 mounts[targetdir]["uuid"] = self.pathmapper.pdh_to_uuid[pdh]
 140             if len(sp) == 2:
 141                 if tp == "Directory":
 142                     path = sp[1]
 143                 else:
 144                     path = os.path.dirname(sp[1])
 145                 if path and path != "/":
 146                     mounts[targetdir]["path"] = path
 147             prevdir = targetdir + "/"
 148
 149         intermediate_collection_info = arvados_cwl.util.get_intermediate_collection_info(self.name, runtimeContext.current_container, runtimeContext.intermediate_output_ttl)
 150
 151         with Perf(metrics, "generatefiles %s" % self.name):
 152             if self.generatefiles["listing"]:
 153                 vwd = arvados.collection.Collection(api_client=self.arvrunner.api,
 154                                                     keep_client=self.arvrunner.keep_client,
 155                                                     num_retries=self.arvrunner.num_retries)
 156                 generatemapper = NoFollowPathMapper(self.generatefiles["listing"], "", "",
 157                                                     separateDirs=False)
 158
 159                 sorteditems = sorted(generatemapper.items(), key=lambda n: n[1].target)
 160
 161                 logger.debug("generatemapper is %s", sorteditems)
 162
 163                 with Perf(metrics, "createfiles %s" % self.name):
 164                     for f, p in sorteditems:
 165                         if not p.target:
 166                             continue
 167
 168                         if p.target.startswith("/"):
 169                             dst = p.target[len(self.outdir)+1:] if p.target.startswith(self.outdir+"/") else p.target[1:]
 170                         else:
 171                             dst = p.target
 172
 173                         if p.type in ("File", "Directory", "WritableFile", "WritableDirectory"):
 174                             if p.resolved.startswith("_:"):
 175                                 vwd.mkdirs(dst)
 176                             else:
 177                                 source, path = self.arvrunner.fs_access.get_collection(p.resolved)
 178                                 vwd.copy(path or ".", dst, source_collection=source)
 179                         elif p.type == "CreateFile":
 180                             if self.arvrunner.secret_store.has_secret(p.resolved):
 181                                 mountpoint = p.target if p.target.startswith("/") else os.path.join(self.outdir, p.target)
 182                                 secret_mounts[mountpoint] = {
 183                                     "kind": "text",
 184                                     "content": self.arvrunner.secret_store.retrieve(p.resolved)
 185                                 }
 186                             else:
 187                                 with vwd.open(dst, "w") as n:
 188                                     n.write(p.resolved)
 189
 190                 def keepemptydirs(p):
 191                     if isinstance(p, arvados.collection.RichCollectionBase):
 192                         if len(p) == 0:
 193                             p.open(".keep", "w").close()
 194                         else:
 195                             for c in p:
 196                                 keepemptydirs(p[c])
 197
 198                 keepemptydirs(vwd)
 199
 200                 if not runtimeContext.current_container:
 201                     runtimeContext.current_container = arvados_cwl.util.get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger)
 202                 vwd.save_new(name=info["name"],
 203                              owner_uuid=runtimeContext.project_uuid,
 204                              ensure_unique_name=True,
 205                              trash_at=intermediate_collection_info["trash_at"],
 206                              properties=intermediate_collection_info["properties"])
 207
 208                 prev = None
 209                 for f, p in sorteditems:
 210                     if (not p.target or self.arvrunner.secret_store.has_secret(p.resolved) or
 211                         (prev is not None and p.target.startswith(prev))):
 212                         continue
 213                     if p.target.startswith("/"):
 214                         dst = p.target[len(self.outdir)+1:] if p.target.startswith(self.outdir+"/") else p.target[1:]
 215                     else:
 216                         dst = p.target
 217                     mountpoint = p.target if p.target.startswith("/") else os.path.join(self.outdir, p.target)
 218                     mounts[mountpoint] = {"kind": "collection",
 219                                           "portable_data_hash": vwd.portable_data_hash(),
 220                                           "path": dst}
 221                     if p.type.startswith("Writable"):
 222                         mounts[mountpoint]["writable"] = True
 223                     prev = p.target + "/"
 224
 225         container_request["environment"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
 226         if self.environment:
 227             container_request["environment"].update(self.environment)
 228
 229         if self.stdin:
 230             sp = self.stdin[6:].split("/", 1)
 231             mounts["stdin"] = {"kind": "collection",
 232                                 "portable_data_hash": sp[0],
 233                                 "path": sp[1]}
 234
 235         if self.stderr:
 236             mounts["stderr"] = {"kind": "file",
 237                                 "path": "%s/%s" % (self.outdir, self.stderr)}
 238
 239         if self.stdout:
 240             mounts["stdout"] = {"kind": "file",
 241                                 "path": "%s/%s" % (self.outdir, self.stdout)}
 242
 243         (docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
 244
 245         container_request["container_image"] = arv_docker_get_image(self.arvrunner.api,
 246                                                                     docker_req,
 247                                                                     runtimeContext.pull_image,
 248                                                                     runtimeContext.project_uuid,
 249                                                                     runtimeContext.force_docker_pull,
 250                                                                     runtimeContext.tmp_outdir_prefix,
 251                                                                     runtimeContext.match_local_docker,
 252                                                                     runtimeContext.copy_deps)
 253
 254         network_req, _ = self.get_requirement("NetworkAccess")
 255         if network_req:
 256             runtime_constraints["API"] = network_req["networkAccess"]
 257
 258         api_req, _ = self.get_requirement("http://arvados.org/cwl#APIRequirement")
 259         if api_req:
 260             runtime_constraints["API"] = True
 261
 262         runtime_req, _ = self.get_requirement("http://arvados.org/cwl#RuntimeConstraints")
 263         if runtime_req:
 264             if "keep_cache" in runtime_req:
 265                 runtime_constraints["keep_cache_ram"] = math.ceil(runtime_req["keep_cache"] * 2**20)
 266             if "outputDirType" in runtime_req:
 267                 if runtime_req["outputDirType"] == "local_output_dir":
 268                     # Currently the default behavior.
 269                     pass
 270                 elif runtime_req["outputDirType"] == "keep_output_dir":
 271                     mounts[self.outdir]= {
 272                         "kind": "collection",
 273                         "writable": True
 274                     }
 275
 276         partition_req, _ = self.get_requirement("http://arvados.org/cwl#PartitionRequirement")
 277         if partition_req:
 278             scheduling_parameters["partitions"] = aslist(partition_req["partition"])
 279
 280         intermediate_output_req, _ = self.get_requirement("http://arvados.org/cwl#IntermediateOutput")
 281         if intermediate_output_req:
 282             self.output_ttl = intermediate_output_req["outputTTL"]
 283         else:
 284             self.output_ttl = self.arvrunner.intermediate_output_ttl
 285
 286         if self.output_ttl < 0:
 287             raise WorkflowException("Invalid value %d for output_ttl, cannot be less than zero" % container_request["output_ttl"])
 288
 289
 290         if self.arvrunner.api._rootDesc["revision"] >= "20210628":
 291             storage_class_req, _ = self.get_requirement("http://arvados.org/cwl#OutputStorageClass")
 292             if storage_class_req and storage_class_req.get("intermediateStorageClass"):
 293                 container_request["output_storage_classes"] = aslist(storage_class_req["intermediateStorageClass"])
 294             else:
 295                 container_request["output_storage_classes"] = runtimeContext.intermediate_storage_classes.strip().split(",")
 296
 297         cuda_req, _ = self.get_requirement("http://commonwl.org/cwltool#CUDARequirement")
 298         if cuda_req:
 299             runtime_constraints["cuda"] = {
 300                 "device_count": resources.get("cudaDeviceCount", 1),
 301                 "driver_version": cuda_req["cudaVersionMin"],
 302                 "hardware_capability": aslist(cuda_req["cudaComputeCapability"])[0]
 303             }
 304
 305         if runtimeContext.enable_preemptible is False:
 306             scheduling_parameters["preemptible"] = False
 307         else:
 308             preemptible_req, _ = self.get_requirement("http://arvados.org/cwl#UsePreemptible")
 309             if preemptible_req:
 310                 scheduling_parameters["preemptible"] = preemptible_req["usePreemptible"]
 311             elif runtimeContext.enable_preemptible is True:
 312                 scheduling_parameters["preemptible"] = True
 313             elif runtimeContext.enable_preemptible is None:
 314                 pass
 315
 316         if self.timelimit is not None and self.timelimit > 0:
 317             scheduling_parameters["max_run_time"] = self.timelimit
 318
 319         extra_submit_params = {}
 320         if runtimeContext.submit_runner_cluster:
 321             extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster
 322
 323         container_request["output_name"] = "Output for step %s" % (self.name)
 324         container_request["output_ttl"] = self.output_ttl
 325         container_request["mounts"] = mounts
 326         container_request["secret_mounts"] = secret_mounts
 327         container_request["runtime_constraints"] = runtime_constraints
 328         container_request["scheduling_parameters"] = scheduling_parameters
 329
 330         enable_reuse = runtimeContext.enable_reuse
 331         if enable_reuse:
 332             reuse_req, _ = self.get_requirement("WorkReuse")
 333             if reuse_req:
 334                 enable_reuse = reuse_req["enableReuse"]
 335             reuse_req, _ = self.get_requirement("http://arvados.org/cwl#ReuseRequirement")
 336             if reuse_req:
 337                 enable_reuse = reuse_req["enableReuse"]
 338         container_request["use_existing"] = enable_reuse
 339
 340         properties_req, _ = self.get_requirement("http://arvados.org/cwl#ProcessProperties")
 341         if properties_req:
 342             for pr in properties_req["processProperties"]:
 343                 container_request["properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"])
 344
 345         output_properties_req, _ = self.get_requirement("http://arvados.org/cwl#OutputCollectionProperties")
 346         if output_properties_req:
 347             for pr in output_properties_req["processProperties"]:
 348                 container_request["output_properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"])
 349
 350         output_properties.update(intermediate_collection_info["properties"])
 351
 352         if runtimeContext.runnerjob.startswith("arvwf:"):
 353             wfuuid = runtimeContext.runnerjob[6:runtimeContext.runnerjob.index("#")]
 354             wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(num_retries=self.arvrunner.num_retries)
 355             if container_request["name"] == "main":
 356                 container_request["name"] = wfrecord["name"]
 357             container_request["properties"]["template_uuid"] = wfuuid
 358
 359         self.output_callback = self.arvrunner.get_wrapped_callback(self.output_callback)
 360
 361         try:
 362             if runtimeContext.submit_request_uuid:
 363                 response = self.arvrunner.api.container_requests().update(
 364                     uuid=runtimeContext.submit_request_uuid,
 365                     body=container_request,
 366                     **extra_submit_params
 367                 ).execute(num_retries=self.arvrunner.num_retries)
 368             else:
 369                 response = self.arvrunner.api.container_requests().create(
 370                     body=container_request,
 371                     **extra_submit_params
 372                 ).execute(num_retries=self.arvrunner.num_retries)
 373
 374             self.uuid = response["uuid"]
 375             self.arvrunner.process_submitted(self)
 376
 377             if response["state"] == "Final":
 378                 logger.info("%s reused container %s", self.arvrunner.label(self), response["container_uuid"])
 379             else:
 380                 logger.info("%s %s state is %s", self.arvrunner.label(self), response["uuid"], response["state"])
 381         except Exception as e:
 382             logger.exception("%s error submitting container\n%s", self.arvrunner.label(self), e)
 383             logger.debug("Container request was %s", container_request)
 384             self.output_callback({}, "permanentFail")
 385
 386     def done(self, record):
 387         outputs = {}
 388         try:
 389             container = self.arvrunner.api.containers().get(
 390                 uuid=record["container_uuid"]
 391             ).execute(num_retries=self.arvrunner.num_retries)
 392             if container["state"] == "Complete":
 393                 rcode = container["exit_code"]
 394                 if self.successCodes and rcode in self.successCodes:
 395                     processStatus = "success"
 396                 elif self.temporaryFailCodes and rcode in self.temporaryFailCodes:
 397                     processStatus = "temporaryFail"
 398                 elif self.permanentFailCodes and rcode in self.permanentFailCodes:
 399                     processStatus = "permanentFail"
 400                 elif rcode == 0:
 401                     processStatus = "success"
 402                 else:
 403                     processStatus = "permanentFail"
 404
 405                 if rcode == 137:
 406                     logger.warning("%s Container may have been killed for using too much RAM.  Try resubmitting with a higher 'ramMin'.",
 407                                  self.arvrunner.label(self))
 408             else:
 409                 processStatus = "permanentFail"
 410
 411             if processStatus == "permanentFail" and record["log_uuid"]:
 412                 logc = arvados.collection.CollectionReader(record["log_uuid"],
 413                                                            api_client=self.arvrunner.api,
 414                                                            keep_client=self.arvrunner.keep_client,
 415                                                            num_retries=self.arvrunner.num_retries)
 416                 label = self.arvrunner.label(self)
 417                 done.logtail(
 418                     logc, logger.error,
 419                     "%s (%s) error log:" % (label, record["uuid"]), maxlen=40)
 420
 421             if record["output_uuid"]:
 422                 if self.arvrunner.trash_intermediate or self.arvrunner.intermediate_output_ttl:
 423                     # Compute the trash time to avoid requesting the collection record.
 424                     trash_at = ciso8601.parse_datetime_as_naive(record["modified_at"]) + datetime.timedelta(0, self.arvrunner.intermediate_output_ttl)
 425                     aftertime = " at %s" % trash_at.strftime("%Y-%m-%d %H:%M:%S UTC") if self.arvrunner.intermediate_output_ttl else ""
 426                     orpart = ", or" if self.arvrunner.trash_intermediate and self.arvrunner.intermediate_output_ttl else ""
 427                     oncomplete = " upon successful completion of the workflow" if self.arvrunner.trash_intermediate else ""
 428                     logger.info("%s Intermediate output %s (%s) will be trashed%s%s%s." % (
 429                         self.arvrunner.label(self), record["output_uuid"], container["output"], aftertime, orpart, oncomplete))
 430                 self.arvrunner.add_intermediate_output(record["output_uuid"])
 431
 432             if container["output"]:
 433                 outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
 434         except WorkflowException as e:
 435             # Only include a stack trace if in debug mode.
 436             # A stack trace may obfuscate more useful output about the workflow.
 437             logger.error("%s unable to collect output from %s:\n%s",
 438                          self.arvrunner.label(self), container["output"], e, exc_info=(e if self.arvrunner.debug else False))
 439             processStatus = "permanentFail"
 440         except Exception:
 441             logger.exception("%s while getting output object:", self.arvrunner.label(self))
 442             processStatus = "permanentFail"
 443         finally:
 444             self.output_callback(outputs, processStatus)
 445
 446
 447 class RunnerContainer(Runner):
 448     """Submit and manage a container that runs arvados-cwl-runner."""
 449
 450     def arvados_job_spec(self, runtimeContext):
 451         """Create an Arvados container request for this workflow.
 452
 453         The returned dict can be used to create a container passed as
 454         the +body+ argument to container_requests().create().
 455         """
 456
 457         adjustDirObjs(self.job_order, trim_listing)
 458         visit_class(self.job_order, ("File", "Directory"), trim_anonymous_location)
 459         visit_class(self.job_order, ("File", "Directory"), remove_redundant_fields)
 460
 461         secret_mounts = {}
 462         for param in sorted(self.job_order.keys()):
 463             if self.secret_store.has_secret(self.job_order[param]):
 464                 mnt = "/secrets/s%d" % len(secret_mounts)
 465                 secret_mounts[mnt] = {
 466                     "kind": "text",
 467                     "content": self.secret_store.retrieve(self.job_order[param])
 468                 }
 469                 self.job_order[param] = {"$include": mnt}
 470
 471         container_req = {
 472             "name": self.name,
 473             "output_path": "/var/spool/cwl",
 474             "cwd": "/var/spool/cwl",
 475             "priority": self.priority,
 476             "state": "Committed",
 477             "container_image": arvados_jobs_image(self.arvrunner, self.jobs_image, runtimeContext),
 478             "mounts": {
 479                 "/var/lib/cwl/cwl.input.json": {
 480                     "kind": "json",
 481                     "content": self.job_order
 482                 },
 483                 "stdout": {
 484                     "kind": "file",
 485                     "path": "/var/spool/cwl/cwl.output.json"
 486                 },
 487                 "/var/spool/cwl": {
 488                     "kind": "collection",
 489                     "writable": True
 490                 }
 491             },
 492             "secret_mounts": secret_mounts,
 493             "runtime_constraints": {
 494                 "vcpus": math.ceil(self.submit_runner_cores),
 495                 "ram": 1024*1024 * (math.ceil(self.submit_runner_ram) + math.ceil(self.collection_cache_size)),
 496                 "API": True
 497             },
 498             "use_existing": False, # Never reuse the runner container - see #15497.
 499             "properties": {}
 500         }
 501
 502         if self.embedded_tool.tool.get("id", "").startswith("keep:"):
 503             sp = self.embedded_tool.tool["id"].split('/')
 504             workflowcollection = sp[0][5:]
 505             workflowname = "/".join(sp[1:])
 506             workflowpath = "/var/lib/cwl/workflow/%s" % workflowname
 507             container_req["mounts"]["/var/lib/cwl/workflow"] = {
 508                 "kind": "collection",
 509                 "portable_data_hash": "%s" % workflowcollection
 510             }
 511         else:
 512             packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map, runtimeContext)
 513             workflowpath = "/var/lib/cwl/workflow.json#main"
 514             container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
 515                 "kind": "json",
 516                 "content": packed
 517             }
 518             if self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
 519                 container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
 520
 521         properties_req, _ = self.embedded_tool.get_requirement("http://arvados.org/cwl#ProcessProperties")
 522         if properties_req:
 523             builder = make_builder(self.job_order, self.embedded_tool.hints, self.embedded_tool.requirements, runtimeContext, self.embedded_tool.metadata)
 524             for pr in properties_req["processProperties"]:
 525                 container_req["properties"][pr["propertyName"]] = builder.do_eval(pr["propertyValue"])
 526
 527         # --local means execute the workflow instead of submitting a container request
 528         # --api=containers means use the containers API
 529         # --no-log-timestamps means don't add timestamps (the logging infrastructure does this)
 530         # --disable-validate because we already validated so don't need to do it again
 531         # --eval-timeout is the timeout for javascript invocation
 532         # --parallel-task-count is the number of threads to use for job submission
 533         # --enable/disable-reuse sets desired job reuse
 534         # --collection-cache-size sets aside memory to store collections
 535         command = ["arvados-cwl-runner",
 536                    "--local",
 537                    "--api=containers",
 538                    "--no-log-timestamps",
 539                    "--disable-validate",
 540                    "--disable-color",
 541                    "--eval-timeout=%s" % self.arvrunner.eval_timeout,
 542                    "--thread-count=%s" % self.arvrunner.thread_count,
 543                    "--enable-reuse" if self.enable_reuse else "--disable-reuse",
 544                    "--collection-cache-size=%s" % self.collection_cache_size]
 545
 546         if self.output_name:
 547             command.append("--output-name=" + self.output_name)
 548             container_req["output_name"] = self.output_name
 549
 550         if self.output_tags:
 551             command.append("--output-tags=" + self.output_tags)
 552
 553         if runtimeContext.debug:
 554             command.append("--debug")
 555
 556         if runtimeContext.storage_classes != "default" and runtimeContext.storage_classes:
 557             command.append("--storage-classes=" + runtimeContext.storage_classes)
 558
 559         if runtimeContext.intermediate_storage_classes != "default" and runtimeContext.intermediate_storage_classes:
 560             command.append("--intermediate-storage-classes=" + runtimeContext.intermediate_storage_classes)
 561
 562         if runtimeContext.on_error:
 563             command.append("--on-error=" + self.on_error)
 564
 565         if runtimeContext.intermediate_output_ttl:
 566             command.append("--intermediate-output-ttl=%d" % runtimeContext.intermediate_output_ttl)
 567
 568         if runtimeContext.trash_intermediate:
 569             command.append("--trash-intermediate")
 570
 571         if runtimeContext.project_uuid:
 572             command.append("--project-uuid="+runtimeContext.project_uuid)
 573
 574         if self.enable_dev:
 575             command.append("--enable-dev")
 576
 577         if runtimeContext.enable_preemptible is True:
 578             command.append("--enable-preemptible")
 579
 580         if runtimeContext.enable_preemptible is False:
 581             command.append("--disable-preemptible")
 582
 583         command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
 584
 585         container_req["command"] = command
 586
 587         return container_req
 588
 589
 590     def run(self, runtimeContext):
 591         runtimeContext.keepprefix = "keep:"
 592         job_spec = self.arvados_job_spec(runtimeContext)
 593         if runtimeContext.project_uuid:
 594             job_spec["owner_uuid"] = runtimeContext.project_uuid
 595
 596         extra_submit_params = {}
 597         if runtimeContext.submit_runner_cluster:
 598             extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster
 599
 600         if runtimeContext.submit_request_uuid:
 601             if "cluster_id" in extra_submit_params:
 602                 # Doesn't make sense for "update" and actually fails
 603                 del extra_submit_params["cluster_id"]
 604             response = self.arvrunner.api.container_requests().update(
 605                 uuid=runtimeContext.submit_request_uuid,
 606                 body=job_spec,
 607                 **extra_submit_params
 608             ).execute(num_retries=self.arvrunner.num_retries)
 609         else:
 610             response = self.arvrunner.api.container_requests().create(
 611                 body=job_spec,
 612                 **extra_submit_params
 613             ).execute(num_retries=self.arvrunner.num_retries)
 614
 615         self.uuid = response["uuid"]
 616         self.arvrunner.process_submitted(self)
 617
 618         logger.info("%s submitted container_request %s", self.arvrunner.label(self), response["uuid"])
 619
 620         workbench1 = self.arvrunner.api.config()["Services"]["Workbench1"]["ExternalURL"]
 621         workbench2 = self.arvrunner.api.config()["Services"]["Workbench2"]["ExternalURL"]
 622         url = ""
 623         if workbench2:
 624             url = "{}processes/{}".format(workbench2, response["uuid"])
 625         elif workbench1:
 626             url = "{}container_requests/{}".format(workbench1, response["uuid"])
 627         if url:
 628             logger.info("Monitor workflow progress at %s", url)
 629
 630
 631     def done(self, record):
 632         try:
 633             container = self.arvrunner.api.containers().get(
 634                 uuid=record["container_uuid"]
 635             ).execute(num_retries=self.arvrunner.num_retries)
 636             container["log"] = record["log_uuid"]
 637         except Exception:
 638             logger.exception("%s while getting runner container", self.arvrunner.label(self))
 639             self.arvrunner.output_callback({}, "permanentFail")
 640         else:
 641             super(RunnerContainer, self).done(container)