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