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, runtimeContext):
  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         with Perf(metrics, "generatefiles %s" % self.name):
 150             if self.generatefiles["listing"]:
 151                 vwd = arvados.collection.Collection(api_client=self.arvrunner.api,
 152                                                     keep_client=self.arvrunner.keep_client,
 153                                                     num_retries=self.arvrunner.num_retries)
 154                 generatemapper = NoFollowPathMapper(self.generatefiles["listing"], "", "",
 155                                                     separateDirs=False)
 156
 157                 sorteditems = sorted(generatemapper.items(), key=lambda n: n[1].target)
 158
 159                 logger.debug("generatemapper is %s", sorteditems)
 160
 161                 with Perf(metrics, "createfiles %s" % self.name):
 162                     for f, p in sorteditems:
 163                         if not p.target:
 164                             continue
 165
 166                         if p.target.startswith("/"):
 167                             dst = p.target[len(self.outdir)+1:] if p.target.startswith(self.outdir+"/") else p.target[1:]
 168                         else:
 169                             dst = p.target
 170
 171                         if p.type in ("File", "Directory", "WritableFile", "WritableDirectory"):
 172                             if p.resolved.startswith("_:"):
 173                                 vwd.mkdirs(dst)
 174                             else:
 175                                 source, path = self.arvrunner.fs_access.get_collection(p.resolved)
 176                                 vwd.copy(path or ".", dst, source_collection=source)
 177                         elif p.type == "CreateFile":
 178                             if self.arvrunner.secret_store.has_secret(p.resolved):
 179                                 mountpoint = p.target if p.target.startswith("/") else os.path.join(self.outdir, p.target)
 180                                 secret_mounts[mountpoint] = {
 181                                     "kind": "text",
 182                                     "content": self.arvrunner.secret_store.retrieve(p.resolved)
 183                                 }
 184                             else:
 185                                 with vwd.open(dst, "w") as n:
 186                                     n.write(p.resolved)
 187
 188                 def keepemptydirs(p):
 189                     if isinstance(p, arvados.collection.RichCollectionBase):
 190                         if len(p) == 0:
 191                             p.open(".keep", "w").close()
 192                         else:
 193                             for c in p:
 194                                 keepemptydirs(p[c])
 195
 196                 keepemptydirs(vwd)
 197
 198                 if not runtimeContext.current_container:
 199                     runtimeContext.current_container = arvados_cwl.util.get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger)
 200                 info = arvados_cwl.util.get_intermediate_collection_info(self.name, runtimeContext.current_container, runtimeContext.intermediate_output_ttl)
 201                 vwd.save_new(name=info["name"],
 202                              owner_uuid=runtimeContext.project_uuid,
 203                              ensure_unique_name=True,
 204                              trash_at=info["trash_at"],
 205                              properties=info["properties"])
 206
 207                 prev = None
 208                 for f, p in sorteditems:
 209                     if (not p.target or self.arvrunner.secret_store.has_secret(p.resolved) or
 210                         (prev is not None and p.target.startswith(prev))):
 211                         continue
 212                     if p.target.startswith("/"):
 213                         dst = p.target[len(self.outdir)+1:] if p.target.startswith(self.outdir+"/") else p.target[1:]
 214                     else:
 215                         dst = p.target
 216                     mountpoint = p.target if p.target.startswith("/") else os.path.join(self.outdir, p.target)
 217                     mounts[mountpoint] = {"kind": "collection",
 218                                           "portable_data_hash": vwd.portable_data_hash(),
 219                                           "path": dst}
 220                     if p.type.startswith("Writable"):
 221                         mounts[mountpoint]["writable"] = True
 222                     prev = p.target + "/"
 223
 224         container_request["environment"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
 225         if self.environment:
 226             container_request["environment"].update(self.environment)
 227
 228         if self.stdin:
 229             sp = self.stdin[6:].split("/", 1)
 230             mounts["stdin"] = {"kind": "collection",
 231                                 "portable_data_hash": sp[0],
 232                                 "path": sp[1]}
 233
 234         if self.stderr:
 235             mounts["stderr"] = {"kind": "file",
 236                                 "path": "%s/%s" % (self.outdir, self.stderr)}
 237
 238         if self.stdout:
 239             mounts["stdout"] = {"kind": "file",
 240                                 "path": "%s/%s" % (self.outdir, self.stdout)}
 241
 242         (docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
 243
 244         container_request["container_image"] = arv_docker_get_image(self.arvrunner.api,
 245                                                                     docker_req,
 246                                                                     runtimeContext.pull_image,
 247                                                                     runtimeContext.project_uuid,
 248                                                                     runtimeContext.force_docker_pull,
 249                                                                     runtimeContext.tmp_outdir_prefix)
 250
 251         network_req, _ = self.get_requirement("NetworkAccess")
 252         if network_req:
 253             runtime_constraints["API"] = network_req["networkAccess"]
 254
 255         api_req, _ = self.get_requirement("http://arvados.org/cwl#APIRequirement")
 256         if api_req:
 257             runtime_constraints["API"] = True
 258
 259         runtime_req, _ = self.get_requirement("http://arvados.org/cwl#RuntimeConstraints")
 260         if runtime_req:
 261             if "keep_cache" in runtime_req:
 262                 runtime_constraints["keep_cache_ram"] = math.ceil(runtime_req["keep_cache"] * 2**20)
 263             if "outputDirType" in runtime_req:
 264                 if runtime_req["outputDirType"] == "local_output_dir":
 265                     # Currently the default behavior.
 266                     pass
 267                 elif runtime_req["outputDirType"] == "keep_output_dir":
 268                     mounts[self.outdir]= {
 269                         "kind": "collection",
 270                         "writable": True
 271                     }
 272
 273         partition_req, _ = self.get_requirement("http://arvados.org/cwl#PartitionRequirement")
 274         if partition_req:
 275             scheduling_parameters["partitions"] = aslist(partition_req["partition"])
 276
 277         intermediate_output_req, _ = self.get_requirement("http://arvados.org/cwl#IntermediateOutput")
 278         if intermediate_output_req:
 279             self.output_ttl = intermediate_output_req["outputTTL"]
 280         else:
 281             self.output_ttl = self.arvrunner.intermediate_output_ttl
 282
 283         if self.output_ttl < 0:
 284             raise WorkflowException("Invalid value %d for output_ttl, cannot be less than zero" % container_request["output_ttl"])
 285
 286
 287         if self.arvrunner.api._rootDesc["revision"] >= "20210628":
 288             storage_class_req, _ = self.get_requirement("http://arvados.org/cwl#OutputStorageClass")
 289             if storage_class_req and storage_class_req.get("intermediateStorageClass"):
 290                 container_request["output_storage_classes"] = aslist(storage_class_req["intermediateStorageClass"])
 291             else:
 292                 container_request["output_storage_classes"] = runtimeContext.intermediate_storage_classes.strip().split(",")
 293
 294         if self.timelimit is not None and self.timelimit > 0:
 295             scheduling_parameters["max_run_time"] = self.timelimit
 296
 297         extra_submit_params = {}
 298         if runtimeContext.submit_runner_cluster:
 299             extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster
 300
 301         container_request["output_name"] = "Output for step %s" % (self.name)
 302         container_request["output_ttl"] = self.output_ttl
 303         container_request["mounts"] = mounts
 304         container_request["secret_mounts"] = secret_mounts
 305         container_request["runtime_constraints"] = runtime_constraints
 306         container_request["scheduling_parameters"] = scheduling_parameters
 307
 308         enable_reuse = runtimeContext.enable_reuse
 309         if enable_reuse:
 310             reuse_req, _ = self.get_requirement("WorkReuse")
 311             if reuse_req:
 312                 enable_reuse = reuse_req["enableReuse"]
 313             reuse_req, _ = self.get_requirement("http://arvados.org/cwl#ReuseRequirement")
 314             if reuse_req:
 315                 enable_reuse = reuse_req["enableReuse"]
 316         container_request["use_existing"] = enable_reuse
 317
 318         properties_req, _ = self.get_requirement("http://arvados.org/cwl#ProcessProperties")
 319         if properties_req:
 320             for pr in properties_req["processProperties"]:
 321                 container_request["properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"])
 322
 323         if runtimeContext.runnerjob.startswith("arvwf:"):
 324             wfuuid = runtimeContext.runnerjob[6:runtimeContext.runnerjob.index("#")]
 325             wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(num_retries=self.arvrunner.num_retries)
 326             if container_request["name"] == "main":
 327                 container_request["name"] = wfrecord["name"]
 328             container_request["properties"]["template_uuid"] = wfuuid
 329
 330         self.output_callback = self.arvrunner.get_wrapped_callback(self.output_callback)
 331
 332         try:
 333             if runtimeContext.submit_request_uuid:
 334                 response = self.arvrunner.api.container_requests().update(
 335                     uuid=runtimeContext.submit_request_uuid,
 336                     body=container_request,
 337                     **extra_submit_params
 338                 ).execute(num_retries=self.arvrunner.num_retries)
 339             else:
 340                 response = self.arvrunner.api.container_requests().create(
 341                     body=container_request,
 342                     **extra_submit_params
 343                 ).execute(num_retries=self.arvrunner.num_retries)
 344
 345             self.uuid = response["uuid"]
 346             self.arvrunner.process_submitted(self)
 347
 348             if response["state"] == "Final":
 349                 logger.info("%s reused container %s", self.arvrunner.label(self), response["container_uuid"])
 350             else:
 351                 logger.info("%s %s state is %s", self.arvrunner.label(self), response["uuid"], response["state"])
 352         except Exception as e:
 353             logger.exception("%s error submitting container\n%s", self.arvrunner.label(self), e)
 354             logger.debug("Container request was %s", container_request)
 355             self.output_callback({}, "permanentFail")
 356
 357     def done(self, record):
 358         outputs = {}
 359         try:
 360             container = self.arvrunner.api.containers().get(
 361                 uuid=record["container_uuid"]
 362             ).execute(num_retries=self.arvrunner.num_retries)
 363             if container["state"] == "Complete":
 364                 rcode = container["exit_code"]
 365                 if self.successCodes and rcode in self.successCodes:
 366                     processStatus = "success"
 367                 elif self.temporaryFailCodes and rcode in self.temporaryFailCodes:
 368                     processStatus = "temporaryFail"
 369                 elif self.permanentFailCodes and rcode in self.permanentFailCodes:
 370                     processStatus = "permanentFail"
 371                 elif rcode == 0:
 372                     processStatus = "success"
 373                 else:
 374                     processStatus = "permanentFail"
 375             else:
 376                 processStatus = "permanentFail"
 377
 378             if processStatus == "permanentFail" and record["log_uuid"]:
 379                 logc = arvados.collection.CollectionReader(record["log_uuid"],
 380                                                            api_client=self.arvrunner.api,
 381                                                            keep_client=self.arvrunner.keep_client,
 382                                                            num_retries=self.arvrunner.num_retries)
 383                 label = self.arvrunner.label(self)
 384                 done.logtail(
 385                     logc, logger.error,
 386                     "%s (%s) error log:" % (label, record["uuid"]), maxlen=40)
 387
 388             if record["output_uuid"]:
 389                 if self.arvrunner.trash_intermediate or self.arvrunner.intermediate_output_ttl:
 390                     # Compute the trash time to avoid requesting the collection record.
 391                     trash_at = ciso8601.parse_datetime_as_naive(record["modified_at"]) + datetime.timedelta(0, self.arvrunner.intermediate_output_ttl)
 392                     aftertime = " at %s" % trash_at.strftime("%Y-%m-%d %H:%M:%S UTC") if self.arvrunner.intermediate_output_ttl else ""
 393                     orpart = ", or" if self.arvrunner.trash_intermediate and self.arvrunner.intermediate_output_ttl else ""
 394                     oncomplete = " upon successful completion of the workflow" if self.arvrunner.trash_intermediate else ""
 395                     logger.info("%s Intermediate output %s (%s) will be trashed%s%s%s." % (
 396                         self.arvrunner.label(self), record["output_uuid"], container["output"], aftertime, orpart, oncomplete))
 397                 self.arvrunner.add_intermediate_output(record["output_uuid"])
 398
 399             if container["output"]:
 400                 outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
 401         except WorkflowException as e:
 402             # Only include a stack trace if in debug mode.
 403             # A stack trace may obfuscate more useful output about the workflow.
 404             logger.error("%s unable to collect output from %s:\n%s",
 405                          self.arvrunner.label(self), container["output"], e, exc_info=(e if self.arvrunner.debug else False))
 406             processStatus = "permanentFail"
 407         except Exception:
 408             logger.exception("%s while getting output object:", self.arvrunner.label(self))
 409             processStatus = "permanentFail"
 410         finally:
 411             self.output_callback(outputs, processStatus)
 412
 413
 414 class RunnerContainer(Runner):
 415     """Submit and manage a container that runs arvados-cwl-runner."""
 416
 417     def arvados_job_spec(self, runtimeContext):
 418         """Create an Arvados container request for this workflow.
 419
 420         The returned dict can be used to create a container passed as
 421         the +body+ argument to container_requests().create().
 422         """
 423
 424         adjustDirObjs(self.job_order, trim_listing)
 425         visit_class(self.job_order, ("File", "Directory"), trim_anonymous_location)
 426         visit_class(self.job_order, ("File", "Directory"), remove_redundant_fields)
 427
 428         secret_mounts = {}
 429         for param in sorted(self.job_order.keys()):
 430             if self.secret_store.has_secret(self.job_order[param]):
 431                 mnt = "/secrets/s%d" % len(secret_mounts)
 432                 secret_mounts[mnt] = {
 433                     "kind": "text",
 434                     "content": self.secret_store.retrieve(self.job_order[param])
 435                 }
 436                 self.job_order[param] = {"$include": mnt}
 437
 438         container_req = {
 439             "name": self.name,
 440             "output_path": "/var/spool/cwl",
 441             "cwd": "/var/spool/cwl",
 442             "priority": self.priority,
 443             "state": "Committed",
 444             "container_image": arvados_jobs_image(self.arvrunner, self.jobs_image),
 445             "mounts": {
 446                 "/var/lib/cwl/cwl.input.json": {
 447                     "kind": "json",
 448                     "content": self.job_order
 449                 },
 450                 "stdout": {
 451                     "kind": "file",
 452                     "path": "/var/spool/cwl/cwl.output.json"
 453                 },
 454                 "/var/spool/cwl": {
 455                     "kind": "collection",
 456                     "writable": True
 457                 }
 458             },
 459             "secret_mounts": secret_mounts,
 460             "runtime_constraints": {
 461                 "vcpus": math.ceil(self.submit_runner_cores),
 462                 "ram": 1024*1024 * (math.ceil(self.submit_runner_ram) + math.ceil(self.collection_cache_size)),
 463                 "API": True
 464             },
 465             "use_existing": False, # Never reuse the runner container - see #15497.
 466             "properties": {}
 467         }
 468
 469         if self.embedded_tool.tool.get("id", "").startswith("keep:"):
 470             sp = self.embedded_tool.tool["id"].split('/')
 471             workflowcollection = sp[0][5:]
 472             workflowname = "/".join(sp[1:])
 473             workflowpath = "/var/lib/cwl/workflow/%s" % workflowname
 474             container_req["mounts"]["/var/lib/cwl/workflow"] = {
 475                 "kind": "collection",
 476                 "portable_data_hash": "%s" % workflowcollection
 477             }
 478         else:
 479             packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map)
 480             workflowpath = "/var/lib/cwl/workflow.json#main"
 481             container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
 482                 "kind": "json",
 483                 "content": packed
 484             }
 485             if self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
 486                 container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
 487
 488         properties_req, _ = self.embedded_tool.get_requirement("http://arvados.org/cwl#ProcessProperties")
 489         if properties_req:
 490             builder = make_builder(self.job_order, self.embedded_tool.hints, self.embedded_tool.requirements, runtimeContext, self.embedded_tool.metadata)
 491             for pr in properties_req["processProperties"]:
 492                 container_req["properties"][pr["propertyName"]] = builder.do_eval(pr["propertyValue"])
 493
 494         # --local means execute the workflow instead of submitting a container request
 495         # --api=containers means use the containers API
 496         # --no-log-timestamps means don't add timestamps (the logging infrastructure does this)
 497         # --disable-validate because we already validated so don't need to do it again
 498         # --eval-timeout is the timeout for javascript invocation
 499         # --parallel-task-count is the number of threads to use for job submission
 500         # --enable/disable-reuse sets desired job reuse
 501         # --collection-cache-size sets aside memory to store collections
 502         command = ["arvados-cwl-runner",
 503                    "--local",
 504                    "--api=containers",
 505                    "--no-log-timestamps",
 506                    "--disable-validate",
 507                    "--disable-color",
 508                    "--eval-timeout=%s" % self.arvrunner.eval_timeout,
 509                    "--thread-count=%s" % self.arvrunner.thread_count,
 510                    "--enable-reuse" if self.enable_reuse else "--disable-reuse",
 511                    "--collection-cache-size=%s" % self.collection_cache_size]
 512
 513         if self.output_name:
 514             command.append("--output-name=" + self.output_name)
 515             container_req["output_name"] = self.output_name
 516
 517         if self.output_tags:
 518             command.append("--output-tags=" + self.output_tags)
 519
 520         if runtimeContext.debug:
 521             command.append("--debug")
 522
 523         if runtimeContext.storage_classes != "default":
 524             command.append("--storage-classes=" + runtimeContext.storage_classes)
 525
 526         if runtimeContext.intermediate_storage_classes != "default":
 527             command.append("--intermediate-storage-classes=" + runtimeContext.intermediate_storage_classes)
 528
 529         if self.on_error:
 530             command.append("--on-error=" + self.on_error)
 531
 532         if self.intermediate_output_ttl:
 533             command.append("--intermediate-output-ttl=%d" % self.intermediate_output_ttl)
 534
 535         if self.arvrunner.trash_intermediate:
 536             command.append("--trash-intermediate")
 537
 538         if self.arvrunner.project_uuid:
 539             command.append("--project-uuid="+self.arvrunner.project_uuid)
 540
 541         if self.enable_dev:
 542             command.append("--enable-dev")
 543
 544         command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
 545
 546         container_req["command"] = command
 547
 548         return container_req
 549
 550
 551     def run(self, runtimeContext):
 552         runtimeContext.keepprefix = "keep:"
 553         job_spec = self.arvados_job_spec(runtimeContext)
 554         if self.arvrunner.project_uuid:
 555             job_spec["owner_uuid"] = self.arvrunner.project_uuid
 556
 557         extra_submit_params = {}
 558         if runtimeContext.submit_runner_cluster:
 559             extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster
 560
 561         if runtimeContext.submit_request_uuid:
 562             if "cluster_id" in extra_submit_params:
 563                 # Doesn't make sense for "update" and actually fails
 564                 del extra_submit_params["cluster_id"]
 565             response = self.arvrunner.api.container_requests().update(
 566                 uuid=runtimeContext.submit_request_uuid,
 567                 body=job_spec,
 568                 **extra_submit_params
 569             ).execute(num_retries=self.arvrunner.num_retries)
 570         else:
 571             response = self.arvrunner.api.container_requests().create(
 572                 body=job_spec,
 573                 **extra_submit_params
 574             ).execute(num_retries=self.arvrunner.num_retries)
 575
 576         self.uuid = response["uuid"]
 577         self.arvrunner.process_submitted(self)
 578
 579         logger.info("%s submitted container_request %s", self.arvrunner.label(self), response["uuid"])
 580
 581         workbench1 = self.arvrunner.api.config()["Services"]["Workbench1"]["ExternalURL"]
 582         workbench2 = self.arvrunner.api.config()["Services"]["Workbench2"]["ExternalURL"]
 583         url = ""
 584         if workbench2:
 585             url = "{}processes/{}".format(workbench2, response["uuid"])
 586         elif workbench1:
 587             url = "{}container_requests/{}".format(workbench1, response["uuid"])
 588         if url:
 589             logger.info("Monitor workflow progress at %s", url)
 590
 591
 592     def done(self, record):
 593         try:
 594             container = self.arvrunner.api.containers().get(
 595                 uuid=record["container_uuid"]
 596             ).execute(num_retries=self.arvrunner.num_retries)
 597             container["log"] = record["log_uuid"]
 598         except Exception:
 599             logger.exception("%s while getting runner container", self.arvrunner.label(self))
 600             self.arvrunner.output_callback({}, "permanentFail")
 601         else:
 602             super(RunnerContainer, self).done(container)