sdk/cwl/arvados_cwl/arvcontainer.py

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