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         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 runtimeContext.enable_preemptible is False:
 304             scheduling_parameters["preemptible"] = False
 305         else:
 306             preemptible_req, _ = self.get_requirement("http://arvados.org/cwl#UsePreemptible")
 307             if preemptible_req:
 308                 scheduling_parameters["preemptible"] = preemptible_req["usePreemptible"]
 309             elif runtimeContext.enable_preemptible is True:
 310                 scheduling_parameters["preemptible"] = True
 311             elif runtimeContext.enable_preemptible is None:
 312                 pass
 313
 314         if self.timelimit is not None and self.timelimit > 0:
 315             scheduling_parameters["max_run_time"] = self.timelimit
 316
 317         extra_submit_params = {}
 318         if runtimeContext.submit_runner_cluster:
 319             extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster
 320
 321         container_request["output_name"] = "Output for step %s" % (self.name)
 322         container_request["output_ttl"] = self.output_ttl
 323         container_request["mounts"] = mounts
 324         container_request["secret_mounts"] = secret_mounts
 325         container_request["runtime_constraints"] = runtime_constraints
 326         container_request["scheduling_parameters"] = scheduling_parameters
 327
 328         enable_reuse = runtimeContext.enable_reuse
 329         if enable_reuse:
 330             reuse_req, _ = self.get_requirement("WorkReuse")
 331             if reuse_req:
 332                 enable_reuse = reuse_req["enableReuse"]
 333             reuse_req, _ = self.get_requirement("http://arvados.org/cwl#ReuseRequirement")
 334             if reuse_req:
 335                 enable_reuse = reuse_req["enableReuse"]
 336         container_request["use_existing"] = enable_reuse
 337
 338         properties_req, _ = self.get_requirement("http://arvados.org/cwl#ProcessProperties")
 339         if properties_req:
 340             for pr in properties_req["processProperties"]:
 341                 container_request["properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"])
 342
 343         if runtimeContext.runnerjob.startswith("arvwf:"):
 344             wfuuid = runtimeContext.runnerjob[6:runtimeContext.runnerjob.index("#")]
 345             wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(num_retries=self.arvrunner.num_retries)
 346             if container_request["name"] == "main":
 347                 container_request["name"] = wfrecord["name"]
 348             container_request["properties"]["template_uuid"] = wfuuid
 349
 350         self.output_callback = self.arvrunner.get_wrapped_callback(self.output_callback)
 351
 352         try:
 353             if runtimeContext.submit_request_uuid:
 354                 response = self.arvrunner.api.container_requests().update(
 355                     uuid=runtimeContext.submit_request_uuid,
 356                     body=container_request,
 357                     **extra_submit_params
 358                 ).execute(num_retries=self.arvrunner.num_retries)
 359             else:
 360                 response = self.arvrunner.api.container_requests().create(
 361                     body=container_request,
 362                     **extra_submit_params
 363                 ).execute(num_retries=self.arvrunner.num_retries)
 364
 365             self.uuid = response["uuid"]
 366             self.arvrunner.process_submitted(self)
 367
 368             if response["state"] == "Final":
 369                 logger.info("%s reused container %s", self.arvrunner.label(self), response["container_uuid"])
 370             else:
 371                 logger.info("%s %s state is %s", self.arvrunner.label(self), response["uuid"], response["state"])
 372         except Exception as e:
 373             logger.exception("%s error submitting container\n%s", self.arvrunner.label(self), e)
 374             logger.debug("Container request was %s", container_request)
 375             self.output_callback({}, "permanentFail")
 376
 377     def done(self, record):
 378         outputs = {}
 379         try:
 380             container = self.arvrunner.api.containers().get(
 381                 uuid=record["container_uuid"]
 382             ).execute(num_retries=self.arvrunner.num_retries)
 383             if container["state"] == "Complete":
 384                 rcode = container["exit_code"]
 385                 if self.successCodes and rcode in self.successCodes:
 386                     processStatus = "success"
 387                 elif self.temporaryFailCodes and rcode in self.temporaryFailCodes:
 388                     processStatus = "temporaryFail"
 389                 elif self.permanentFailCodes and rcode in self.permanentFailCodes:
 390                     processStatus = "permanentFail"
 391                 elif rcode == 0:
 392                     processStatus = "success"
 393                 else:
 394                     processStatus = "permanentFail"
 395
 396                 if rcode == 137:
 397                     logger.warning("%s Container may have been killed for using too much RAM.  Try resubmitting with a higher 'ramMin'.",
 398                                  self.arvrunner.label(self))
 399             else:
 400                 processStatus = "permanentFail"
 401
 402             if processStatus == "permanentFail" and record["log_uuid"]:
 403                 logc = arvados.collection.CollectionReader(record["log_uuid"],
 404                                                            api_client=self.arvrunner.api,
 405                                                            keep_client=self.arvrunner.keep_client,
 406                                                            num_retries=self.arvrunner.num_retries)
 407                 label = self.arvrunner.label(self)
 408                 done.logtail(
 409                     logc, logger.error,
 410                     "%s (%s) error log:" % (label, record["uuid"]), maxlen=40)
 411
 412             if record["output_uuid"]:
 413                 if self.arvrunner.trash_intermediate or self.arvrunner.intermediate_output_ttl:
 414                     # Compute the trash time to avoid requesting the collection record.
 415                     trash_at = ciso8601.parse_datetime_as_naive(record["modified_at"]) + datetime.timedelta(0, self.arvrunner.intermediate_output_ttl)
 416                     aftertime = " at %s" % trash_at.strftime("%Y-%m-%d %H:%M:%S UTC") if self.arvrunner.intermediate_output_ttl else ""
 417                     orpart = ", or" if self.arvrunner.trash_intermediate and self.arvrunner.intermediate_output_ttl else ""
 418                     oncomplete = " upon successful completion of the workflow" if self.arvrunner.trash_intermediate else ""
 419                     logger.info("%s Intermediate output %s (%s) will be trashed%s%s%s." % (
 420                         self.arvrunner.label(self), record["output_uuid"], container["output"], aftertime, orpart, oncomplete))
 421                 self.arvrunner.add_intermediate_output(record["output_uuid"])
 422
 423             if container["output"]:
 424                 outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
 425         except WorkflowException as e:
 426             # Only include a stack trace if in debug mode.
 427             # A stack trace may obfuscate more useful output about the workflow.
 428             logger.error("%s unable to collect output from %s:\n%s",
 429                          self.arvrunner.label(self), container["output"], e, exc_info=(e if self.arvrunner.debug else False))
 430             processStatus = "permanentFail"
 431         except Exception:
 432             logger.exception("%s while getting output object:", self.arvrunner.label(self))
 433             processStatus = "permanentFail"
 434         finally:
 435             self.output_callback(outputs, processStatus)
 436
 437
 438 class RunnerContainer(Runner):
 439     """Submit and manage a container that runs arvados-cwl-runner."""
 440
 441     def arvados_job_spec(self, runtimeContext):
 442         """Create an Arvados container request for this workflow.
 443
 444         The returned dict can be used to create a container passed as
 445         the +body+ argument to container_requests().create().
 446         """
 447
 448         adjustDirObjs(self.job_order, trim_listing)
 449         visit_class(self.job_order, ("File", "Directory"), trim_anonymous_location)
 450         visit_class(self.job_order, ("File", "Directory"), remove_redundant_fields)
 451
 452         secret_mounts = {}
 453         for param in sorted(self.job_order.keys()):
 454             if self.secret_store.has_secret(self.job_order[param]):
 455                 mnt = "/secrets/s%d" % len(secret_mounts)
 456                 secret_mounts[mnt] = {
 457                     "kind": "text",
 458                     "content": self.secret_store.retrieve(self.job_order[param])
 459                 }
 460                 self.job_order[param] = {"$include": mnt}
 461
 462         container_req = {
 463             "name": self.name,
 464             "output_path": "/var/spool/cwl",
 465             "cwd": "/var/spool/cwl",
 466             "priority": self.priority,
 467             "state": "Committed",
 468             "container_image": arvados_jobs_image(self.arvrunner, self.jobs_image),
 469             "mounts": {
 470                 "/var/lib/cwl/cwl.input.json": {
 471                     "kind": "json",
 472                     "content": self.job_order
 473                 },
 474                 "stdout": {
 475                     "kind": "file",
 476                     "path": "/var/spool/cwl/cwl.output.json"
 477                 },
 478                 "/var/spool/cwl": {
 479                     "kind": "collection",
 480                     "writable": True
 481                 }
 482             },
 483             "secret_mounts": secret_mounts,
 484             "runtime_constraints": {
 485                 "vcpus": math.ceil(self.submit_runner_cores),
 486                 "ram": 1024*1024 * (math.ceil(self.submit_runner_ram) + math.ceil(self.collection_cache_size)),
 487                 "API": True
 488             },
 489             "use_existing": False, # Never reuse the runner container - see #15497.
 490             "properties": {}
 491         }
 492
 493         if self.embedded_tool.tool.get("id", "").startswith("keep:"):
 494             sp = self.embedded_tool.tool["id"].split('/')
 495             workflowcollection = sp[0][5:]
 496             workflowname = "/".join(sp[1:])
 497             workflowpath = "/var/lib/cwl/workflow/%s" % workflowname
 498             container_req["mounts"]["/var/lib/cwl/workflow"] = {
 499                 "kind": "collection",
 500                 "portable_data_hash": "%s" % workflowcollection
 501             }
 502         else:
 503             packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map)
 504             workflowpath = "/var/lib/cwl/workflow.json#main"
 505             container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
 506                 "kind": "json",
 507                 "content": packed
 508             }
 509             if self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
 510                 container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
 511
 512         properties_req, _ = self.embedded_tool.get_requirement("http://arvados.org/cwl#ProcessProperties")
 513         if properties_req:
 514             builder = make_builder(self.job_order, self.embedded_tool.hints, self.embedded_tool.requirements, runtimeContext, self.embedded_tool.metadata)
 515             for pr in properties_req["processProperties"]:
 516                 container_req["properties"][pr["propertyName"]] = builder.do_eval(pr["propertyValue"])
 517
 518         # --local means execute the workflow instead of submitting a container request
 519         # --api=containers means use the containers API
 520         # --no-log-timestamps means don't add timestamps (the logging infrastructure does this)
 521         # --disable-validate because we already validated so don't need to do it again
 522         # --eval-timeout is the timeout for javascript invocation
 523         # --parallel-task-count is the number of threads to use for job submission
 524         # --enable/disable-reuse sets desired job reuse
 525         # --collection-cache-size sets aside memory to store collections
 526         command = ["arvados-cwl-runner",
 527                    "--local",
 528                    "--api=containers",
 529                    "--no-log-timestamps",
 530                    "--disable-validate",
 531                    "--disable-color",
 532                    "--eval-timeout=%s" % self.arvrunner.eval_timeout,
 533                    "--thread-count=%s" % self.arvrunner.thread_count,
 534                    "--enable-reuse" if self.enable_reuse else "--disable-reuse",
 535                    "--collection-cache-size=%s" % self.collection_cache_size]
 536
 537         if self.output_name:
 538             command.append("--output-name=" + self.output_name)
 539             container_req["output_name"] = self.output_name
 540
 541         if self.output_tags:
 542             command.append("--output-tags=" + self.output_tags)
 543
 544         if runtimeContext.debug:
 545             command.append("--debug")
 546
 547         if runtimeContext.storage_classes != "default" and runtimeContext.storage_classes:
 548             command.append("--storage-classes=" + runtimeContext.storage_classes)
 549
 550         if runtimeContext.intermediate_storage_classes != "default" and runtimeContext.intermediate_storage_classes:
 551             command.append("--intermediate-storage-classes=" + runtimeContext.intermediate_storage_classes)
 552
 553         if self.on_error:
 554             command.append("--on-error=" + self.on_error)
 555
 556         if self.intermediate_output_ttl:
 557             command.append("--intermediate-output-ttl=%d" % self.intermediate_output_ttl)
 558
 559         if self.arvrunner.trash_intermediate:
 560             command.append("--trash-intermediate")
 561
 562         if self.arvrunner.project_uuid:
 563             command.append("--project-uuid="+self.arvrunner.project_uuid)
 564
 565         if self.enable_dev:
 566             command.append("--enable-dev")
 567
 568         if runtimeContext.enable_preemptible is True:
 569             command.append("--enable-preemptible")
 570
 571         if runtimeContext.enable_preemptible is False:
 572             command.append("--disable-preemptible")
 573
 574         command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
 575
 576         container_req["command"] = command
 577
 578         return container_req
 579
 580
 581     def run(self, runtimeContext):
 582         runtimeContext.keepprefix = "keep:"
 583         job_spec = self.arvados_job_spec(runtimeContext)
 584         if self.arvrunner.project_uuid:
 585             job_spec["owner_uuid"] = self.arvrunner.project_uuid
 586
 587         extra_submit_params = {}
 588         if runtimeContext.submit_runner_cluster:
 589             extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster
 590
 591         if runtimeContext.submit_request_uuid:
 592             if "cluster_id" in extra_submit_params:
 593                 # Doesn't make sense for "update" and actually fails
 594                 del extra_submit_params["cluster_id"]
 595             response = self.arvrunner.api.container_requests().update(
 596                 uuid=runtimeContext.submit_request_uuid,
 597                 body=job_spec,
 598                 **extra_submit_params
 599             ).execute(num_retries=self.arvrunner.num_retries)
 600         else:
 601             response = self.arvrunner.api.container_requests().create(
 602                 body=job_spec,
 603                 **extra_submit_params
 604             ).execute(num_retries=self.arvrunner.num_retries)
 605
 606         self.uuid = response["uuid"]
 607         self.arvrunner.process_submitted(self)
 608
 609         logger.info("%s submitted container_request %s", self.arvrunner.label(self), response["uuid"])
 610
 611         workbench1 = self.arvrunner.api.config()["Services"]["Workbench1"]["ExternalURL"]
 612         workbench2 = self.arvrunner.api.config()["Services"]["Workbench2"]["ExternalURL"]
 613         url = ""
 614         if workbench2:
 615             url = "{}processes/{}".format(workbench2, response["uuid"])
 616         elif workbench1:
 617             url = "{}container_requests/{}".format(workbench1, response["uuid"])
 618         if url:
 619             logger.info("Monitor workflow progress at %s", url)
 620
 621
 622     def done(self, record):
 623         try:
 624             container = self.arvrunner.api.containers().get(
 625                 uuid=record["container_uuid"]
 626             ).execute(num_retries=self.arvrunner.num_retries)
 627             container["log"] = record["log_uuid"]
 628         except Exception:
 629             logger.exception("%s while getting runner container", self.arvrunner.label(self))
 630             self.arvrunner.output_callback({}, "permanentFail")
 631         else:
 632             super(RunnerContainer, self).done(container)