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 import re
  19
  20 import arvados_cwl.util
  21 import ruamel.yaml
  22
  23 from cwltool.errors import WorkflowException
  24 from cwltool.process import UnsupportedRequirement, shortname
  25 from cwltool.utils import aslist, adjustFileObjs, adjustDirObjs, visit_class
  26 from cwltool.job import JobBase
  27
  28 import arvados.collection
  29
  30 from .arvdocker import arv_docker_get_image
  31 from . import done
  32 from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location, remove_redundant_fields, make_builder
  33 from .fsaccess import CollectionFetcher
  34 from .pathmapper import NoFollowPathMapper, trim_listing
  35 from .perf import Perf
  36 from ._version import __version__
  37
  38 logger = logging.getLogger('arvados.cwl-runner')
  39 metrics = logging.getLogger('arvados.cwl-runner.metrics')
  40
  41 def cleanup_name_for_collection(name):
  42     return name.replace("/", " ")
  43
  44 class ArvadosContainer(JobBase):
  45     """Submit and manage a Crunch container request for executing a CWL CommandLineTool."""
  46
  47     def __init__(self, runner, job_runtime,
  48                  builder,   # type: Builder
  49                  joborder,  # type: Dict[Text, Union[Dict[Text, Any], List, Text]]
  50                  make_path_mapper,  # type: Callable[..., PathMapper]
  51                  requirements,      # type: List[Dict[Text, Text]]
  52                  hints,     # type: List[Dict[Text, Text]]
  53                  name       # type: Text
  54     ):
  55         super(ArvadosContainer, self).__init__(builder, joborder, make_path_mapper, requirements, hints, name)
  56         self.arvrunner = runner
  57         self.job_runtime = job_runtime
  58         self.running = False
  59         self.uuid = None
  60         self.attempt_count = 0
  61
  62     def update_pipeline_component(self, r):
  63         pass
  64
  65     def _required_env(self):
  66         env = {}
  67         env["HOME"] = self.outdir
  68         env["TMPDIR"] = self.tmpdir
  69         return env
  70
  71     def run(self, toplevelRuntimeContext):
  72         # ArvadosCommandTool subclasses from cwltool.CommandLineTool,
  73         # which calls makeJobRunner() to get a new ArvadosContainer
  74         # object.  The fields that define execution such as
  75         # command_line, environment, etc are set on the
  76         # ArvadosContainer object by CommandLineTool.job() before
  77         # run() is called.
  78
  79         runtimeContext = self.job_runtime
  80
  81         if runtimeContext.submit_request_uuid:
  82             container_request = self.arvrunner.api.container_requests().get(
  83                 uuid=runtimeContext.submit_request_uuid
  84             ).execute(num_retries=self.arvrunner.num_retries)
  85         else:
  86             container_request = {}
  87
  88         container_request["command"] = self.command_line
  89         container_request["name"] = self.name
  90         container_request["output_path"] = self.outdir
  91         container_request["cwd"] = self.outdir
  92         container_request["priority"] = runtimeContext.priority
  93         container_request["state"] = "Uncommitted"
  94         container_request.setdefault("properties", {})
  95
  96         container_request["properties"]["cwl_input"] = self.joborder
  97
  98         runtime_constraints = {}
  99
 100         if runtimeContext.project_uuid:
 101             container_request["owner_uuid"] = runtimeContext.project_uuid
 102
 103         if self.arvrunner.secret_store.has_secret(self.command_line):
 104             raise WorkflowException("Secret material leaked on command line, only file literals may contain secrets")
 105
 106         if self.arvrunner.secret_store.has_secret(self.environment):
 107             raise WorkflowException("Secret material leaked in environment, only file literals may contain secrets")
 108
 109         resources = self.builder.resources
 110         if resources is not None:
 111             runtime_constraints["vcpus"] = math.ceil(resources.get("cores", 1))
 112             runtime_constraints["ram"] = math.ceil(resources.get("ram") * 2**20)
 113
 114         mounts = {
 115             self.outdir: {
 116                 "kind": "tmp",
 117                 "capacity": math.ceil(resources.get("outdirSize", 0) * 2**20)
 118             },
 119             self.tmpdir: {
 120                 "kind": "tmp",
 121                 "capacity": math.ceil(resources.get("tmpdirSize", 0) * 2**20)
 122             }
 123         }
 124         secret_mounts = {}
 125         scheduling_parameters = {}
 126
 127         rf = [self.pathmapper.mapper(f) for f in self.pathmapper.referenced_files]
 128         rf.sort(key=lambda k: k.resolved)
 129         prevdir = None
 130         for resolved, target, tp, stg in rf:
 131             if not stg:
 132                 continue
 133             if prevdir and target.startswith(prevdir):
 134                 continue
 135             if tp == "Directory":
 136                 targetdir = target
 137             else:
 138                 targetdir = os.path.dirname(target)
 139             sp = resolved.split("/", 1)
 140             pdh = sp[0][5:]   # remove "keep:"
 141             mounts[targetdir] = {
 142                 "kind": "collection",
 143                 "portable_data_hash": pdh
 144             }
 145             if pdh in self.pathmapper.pdh_to_uuid:
 146                 mounts[targetdir]["uuid"] = self.pathmapper.pdh_to_uuid[pdh]
 147             if len(sp) == 2:
 148                 if tp == "Directory":
 149                     path = sp[1]
 150                 else:
 151                     path = os.path.dirname(sp[1])
 152                 if path and path != "/":
 153                     mounts[targetdir]["path"] = path
 154             prevdir = targetdir + "/"
 155
 156         intermediate_collection_info = arvados_cwl.util.get_intermediate_collection_info(self.name, runtimeContext.current_container, runtimeContext.intermediate_output_ttl)
 157
 158         with Perf(metrics, "generatefiles %s" % self.name):
 159             if self.generatefiles["listing"]:
 160                 vwd = arvados.collection.Collection(api_client=self.arvrunner.api,
 161                                                     keep_client=self.arvrunner.keep_client,
 162                                                     num_retries=self.arvrunner.num_retries)
 163                 generatemapper = NoFollowPathMapper(self.generatefiles["listing"], "", "",
 164                                                     separateDirs=False)
 165
 166                 sorteditems = sorted(generatemapper.items(), key=lambda n: n[1].target)
 167
 168                 logger.debug("generatemapper is %s", sorteditems)
 169
 170                 with Perf(metrics, "createfiles %s" % self.name):
 171                     for f, p in sorteditems:
 172                         if not p.target:
 173                             continue
 174
 175                         if p.target.startswith("/"):
 176                             dst = p.target[len(self.outdir)+1:] if p.target.startswith(self.outdir+"/") else p.target[1:]
 177                         else:
 178                             dst = p.target
 179
 180                         if p.type in ("File", "Directory", "WritableFile", "WritableDirectory"):
 181                             if p.resolved.startswith("_:"):
 182                                 vwd.mkdirs(dst)
 183                             else:
 184                                 source, path = self.arvrunner.fs_access.get_collection(p.resolved)
 185                                 vwd.copy(path or ".", dst, source_collection=source)
 186                         elif p.type == "CreateFile":
 187                             if self.arvrunner.secret_store.has_secret(p.resolved):
 188                                 mountpoint = p.target if p.target.startswith("/") else os.path.join(self.outdir, p.target)
 189                                 secret_mounts[mountpoint] = {
 190                                     "kind": "text",
 191                                     "content": self.arvrunner.secret_store.retrieve(p.resolved)
 192                                 }
 193                             else:
 194                                 with vwd.open(dst, "w") as n:
 195                                     n.write(p.resolved)
 196
 197                 def keepemptydirs(p):
 198                     if isinstance(p, arvados.collection.RichCollectionBase):
 199                         if len(p) == 0:
 200                             p.open(".keep", "w").close()
 201                         else:
 202                             for c in p:
 203                                 keepemptydirs(p[c])
 204
 205                 keepemptydirs(vwd)
 206
 207                 if not runtimeContext.current_container:
 208                     runtimeContext.current_container = arvados_cwl.util.get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger)
 209                 vwd.save_new(name=intermediate_collection_info["name"],
 210                              owner_uuid=runtimeContext.project_uuid,
 211                              ensure_unique_name=True,
 212                              trash_at=intermediate_collection_info["trash_at"],
 213                              properties=intermediate_collection_info["properties"])
 214
 215                 prev = None
 216                 for f, p in sorteditems:
 217                     if (not p.target or self.arvrunner.secret_store.has_secret(p.resolved) or
 218                         (prev is not None and p.target.startswith(prev))):
 219                         continue
 220                     if p.target.startswith("/"):
 221                         dst = p.target[len(self.outdir)+1:] if p.target.startswith(self.outdir+"/") else p.target[1:]
 222                     else:
 223                         dst = p.target
 224                     mountpoint = p.target if p.target.startswith("/") else os.path.join(self.outdir, p.target)
 225                     mounts[mountpoint] = {"kind": "collection",
 226                                           "portable_data_hash": vwd.portable_data_hash(),
 227                                           "path": dst}
 228                     if p.type.startswith("Writable"):
 229                         mounts[mountpoint]["writable"] = True
 230                     prev = p.target + "/"
 231
 232         container_request["environment"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
 233         if self.environment:
 234             container_request["environment"].update(self.environment)
 235
 236         if self.stdin:
 237             sp = self.stdin[6:].split("/", 1)
 238             mounts["stdin"] = {"kind": "collection",
 239                                 "portable_data_hash": sp[0],
 240                                 "path": sp[1]}
 241
 242         if self.stderr:
 243             mounts["stderr"] = {"kind": "file",
 244                                 "path": "%s/%s" % (self.outdir, self.stderr)}
 245
 246         if self.stdout:
 247             mounts["stdout"] = {"kind": "file",
 248                                 "path": "%s/%s" % (self.outdir, self.stdout)}
 249
 250         (docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
 251
 252         container_request["container_image"] = arv_docker_get_image(self.arvrunner.api,
 253                                                                     docker_req,
 254                                                                     runtimeContext.pull_image,
 255                                                                     runtimeContext)
 256
 257         network_req, _ = self.get_requirement("NetworkAccess")
 258         if network_req:
 259             runtime_constraints["API"] = network_req["networkAccess"]
 260
 261         api_req, _ = self.get_requirement("http://arvados.org/cwl#APIRequirement")
 262         if api_req:
 263             runtime_constraints["API"] = True
 264
 265         use_disk_cache = (self.arvrunner.api.config()["Containers"].get("DefaultKeepCacheRAM", 0) == 0)
 266
 267         keep_cache_type_req, _ = self.get_requirement("http://arvados.org/cwl#KeepCacheTypeRequirement")
 268         if keep_cache_type_req:
 269             if "keepCacheType" in keep_cache_type_req:
 270                 if keep_cache_type_req["keepCacheType"] == "ram_cache":
 271                     use_disk_cache = False
 272
 273         runtime_req, _ = self.get_requirement("http://arvados.org/cwl#RuntimeConstraints")
 274         if runtime_req:
 275             if "keep_cache" in runtime_req:
 276                 if use_disk_cache:
 277                     # If DefaultKeepCacheRAM is zero it means we should use disk cache.
 278                     runtime_constraints["keep_cache_disk"] = math.ceil(runtime_req["keep_cache"] * 2**20)
 279                 else:
 280                     runtime_constraints["keep_cache_ram"] = math.ceil(runtime_req["keep_cache"] * 2**20)
 281             if "outputDirType" in runtime_req:
 282                 if runtime_req["outputDirType"] == "local_output_dir":
 283                     # Currently the default behavior.
 284                     pass
 285                 elif runtime_req["outputDirType"] == "keep_output_dir":
 286                     mounts[self.outdir]= {
 287                         "kind": "collection",
 288                         "writable": True
 289                     }
 290
 291         partition_req, _ = self.get_requirement("http://arvados.org/cwl#PartitionRequirement")
 292         if partition_req:
 293             scheduling_parameters["partitions"] = aslist(partition_req["partition"])
 294
 295         intermediate_output_req, _ = self.get_requirement("http://arvados.org/cwl#IntermediateOutput")
 296         if intermediate_output_req:
 297             self.output_ttl = intermediate_output_req["outputTTL"]
 298         else:
 299             self.output_ttl = self.arvrunner.intermediate_output_ttl
 300
 301         if self.output_ttl < 0:
 302             raise WorkflowException("Invalid value %d for output_ttl, cannot be less than zero" % container_request["output_ttl"])
 303
 304
 305         if self.arvrunner.api._rootDesc["revision"] >= "20210628":
 306             storage_class_req, _ = self.get_requirement("http://arvados.org/cwl#OutputStorageClass")
 307             if storage_class_req and storage_class_req.get("intermediateStorageClass"):
 308                 container_request["output_storage_classes"] = aslist(storage_class_req["intermediateStorageClass"])
 309             else:
 310                 container_request["output_storage_classes"] = runtimeContext.intermediate_storage_classes.strip().split(",")
 311
 312         cuda_req, _ = self.get_requirement("http://commonwl.org/cwltool#CUDARequirement")
 313         if cuda_req:
 314             runtime_constraints["cuda"] = {
 315                 "device_count": resources.get("cudaDeviceCount", 1),
 316                 "driver_version": cuda_req["cudaVersionMin"],
 317                 "hardware_capability": aslist(cuda_req["cudaComputeCapability"])[0]
 318             }
 319
 320         if runtimeContext.enable_preemptible is False:
 321             scheduling_parameters["preemptible"] = False
 322         else:
 323             preemptible_req, _ = self.get_requirement("http://arvados.org/cwl#UsePreemptible")
 324             if preemptible_req:
 325                 scheduling_parameters["preemptible"] = preemptible_req["usePreemptible"]
 326             elif runtimeContext.enable_preemptible is True:
 327                 scheduling_parameters["preemptible"] = True
 328             elif runtimeContext.enable_preemptible is None:
 329                 pass
 330
 331         if self.timelimit is not None and self.timelimit > 0:
 332             scheduling_parameters["max_run_time"] = self.timelimit
 333
 334         extra_submit_params = {}
 335         if runtimeContext.submit_runner_cluster:
 336             extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster
 337
 338         container_request["output_name"] = cleanup_name_for_collection("Output from step %s" % (self.name))
 339         container_request["output_ttl"] = self.output_ttl
 340         container_request["mounts"] = mounts
 341         container_request["secret_mounts"] = secret_mounts
 342         container_request["runtime_constraints"] = runtime_constraints
 343         container_request["scheduling_parameters"] = scheduling_parameters
 344
 345         enable_reuse = runtimeContext.enable_reuse
 346         if enable_reuse:
 347             reuse_req, _ = self.get_requirement("WorkReuse")
 348             if reuse_req:
 349                 enable_reuse = reuse_req["enableReuse"]
 350             reuse_req, _ = self.get_requirement("http://arvados.org/cwl#ReuseRequirement")
 351             if reuse_req:
 352                 enable_reuse = reuse_req["enableReuse"]
 353         container_request["use_existing"] = enable_reuse
 354
 355         properties_req, _ = self.get_requirement("http://arvados.org/cwl#ProcessProperties")
 356         if properties_req:
 357             for pr in properties_req["processProperties"]:
 358                 container_request["properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"])
 359
 360         output_properties_req, _ = self.get_requirement("http://arvados.org/cwl#OutputCollectionProperties")
 361         if output_properties_req:
 362             if self.arvrunner.api._rootDesc["revision"] >= "20220510":
 363                 container_request["output_properties"] = {}
 364                 for pr in output_properties_req["outputProperties"]:
 365                     container_request["output_properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"])
 366             else:
 367                 logger.warning("%s API revision is %s, revision %s is required to support setting properties on output collections.",
 368                                self.arvrunner.label(self), self.arvrunner.api._rootDesc["revision"], "20220510")
 369
 370         ramMultiplier = [1]
 371
 372         oom_retry_req, _ = self.get_requirement("http://arvados.org/cwl#OutOfMemoryRetry")
 373         if oom_retry_req and oom_retry_req.get('memoryRetryMultipler'):
 374             ramMultiplier.append(oom_retry_req.get('memoryRetryMultipler'))
 375
 376         if runtimeContext.runnerjob.startswith("arvwf:"):
 377             wfuuid = runtimeContext.runnerjob[6:runtimeContext.runnerjob.index("#")]
 378             wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(num_retries=self.arvrunner.num_retries)
 379             if container_request["name"] == "main":
 380                 container_request["name"] = wfrecord["name"]
 381             container_request["properties"]["template_uuid"] = wfuuid
 382
 383         if self.attempt_count == 0:
 384             self.output_callback = self.arvrunner.get_wrapped_callback(self.output_callback)
 385
 386         try:
 387             ram = runtime_constraints["ram"]
 388
 389             for i in ramMultiplier:
 390                 runtime_constraints["ram"] = ram * i
 391
 392                 if runtimeContext.submit_request_uuid:
 393                     response = self.arvrunner.api.container_requests().update(
 394                         uuid=runtimeContext.submit_request_uuid,
 395                         body=container_request,
 396                         **extra_submit_params
 397                     ).execute(num_retries=self.arvrunner.num_retries)
 398                 else:
 399                     response = self.arvrunner.api.container_requests().create(
 400                         body=container_request,
 401                         **extra_submit_params
 402                     ).execute(num_retries=self.arvrunner.num_retries)
 403                     runtimeContext.submit_request_uuid = response["uuid"]
 404
 405                 if response["container_uuid"] is not None:
 406                     break
 407
 408             if response["container_uuid"] is None:
 409                 runtime_constraints["ram"] = ram * ramMultiplier[self.attempt_count]
 410
 411             container_request["state"] = "Committed"
 412             response = self.arvrunner.api.container_requests().update(
 413                 uuid=runtimeContext.submit_request_uuid,
 414                 body=container_request,
 415                 **extra_submit_params
 416             ).execute(num_retries=self.arvrunner.num_retries)
 417
 418             self.uuid = response["uuid"]
 419             self.arvrunner.process_submitted(self)
 420             self.attempt_count += 1
 421
 422             if response["state"] == "Final":
 423                 logger.info("%s reused container %s", self.arvrunner.label(self), response["container_uuid"])
 424             else:
 425                 logger.info("%s %s state is %s", self.arvrunner.label(self), response["uuid"], response["state"])
 426         except Exception as e:
 427             logger.exception("%s error submitting container\n%s", self.arvrunner.label(self), e)
 428             logger.debug("Container request was %s", container_request)
 429             self.output_callback({}, "permanentFail")
 430
 431     def out_of_memory_retry(self, record, container):
 432         oom_retry_req, _ = self.get_requirement("http://arvados.org/cwl#OutOfMemoryRetry")
 433         if oom_retry_req is None:
 434             return False
 435
 436         # Sometimes it gets killed with no warning
 437         if container["exit_code"] == 137:
 438             return True
 439
 440         logc = arvados.collection.CollectionReader(record["log_uuid"],
 441                                                    api_client=self.arvrunner.api,
 442                                                    keep_client=self.arvrunner.keep_client,
 443                                                    num_retries=self.arvrunner.num_retries)
 444
 445         loglines = [""]
 446         def callback(v1, v2, v3):
 447             loglines[0] = v3
 448
 449         done.logtail(logc, callback, "", maxlen=1000)
 450
 451         # Check allocation failure
 452         oom_matches = oom_retry_req.get('memoryErrorRegex') or r'(bad_alloc|out ?of ?memory|container using over 9.% of memory)'
 453         if re.search(oom_matches, loglines[0], re.IGNORECASE | re.MULTILINE):
 454             return True
 455
 456         return False
 457
 458     def done(self, record):
 459         outputs = {}
 460         retried = False
 461         try:
 462             container = self.arvrunner.api.containers().get(
 463                 uuid=record["container_uuid"]
 464             ).execute(num_retries=self.arvrunner.num_retries)
 465             if container["state"] == "Complete":
 466                 rcode = container["exit_code"]
 467                 if self.successCodes and rcode in self.successCodes:
 468                     processStatus = "success"
 469                 elif self.temporaryFailCodes and rcode in self.temporaryFailCodes:
 470                     processStatus = "temporaryFail"
 471                 elif self.permanentFailCodes and rcode in self.permanentFailCodes:
 472                     processStatus = "permanentFail"
 473                 elif rcode == 0:
 474                     processStatus = "success"
 475                 else:
 476                     processStatus = "permanentFail"
 477
 478                 if processStatus == "permanentFail" and self.attempt_count == 1 and self.out_of_memory_retry(record, container):
 479                     logger.info("%s Container failed with out of memory error, retrying with more RAM.",
 480                                  self.arvrunner.label(self))
 481                     self.job_runtime.submit_request_uuid = None
 482                     self.uuid = None
 483                     self.run(None)
 484                     retried = True
 485                     return
 486
 487                 if rcode == 137:
 488                     logger.warning("%s Container may have been killed for using too much RAM.  Try resubmitting with a higher 'ramMin'.",
 489                                  self.arvrunner.label(self))
 490             else:
 491                 processStatus = "permanentFail"
 492
 493             if processStatus == "permanentFail" and record["log_uuid"]:
 494                 logc = arvados.collection.CollectionReader(record["log_uuid"],
 495                                                            api_client=self.arvrunner.api,
 496                                                            keep_client=self.arvrunner.keep_client,
 497                                                            num_retries=self.arvrunner.num_retries)
 498                 label = self.arvrunner.label(self)
 499                 done.logtail(
 500                     logc, logger.error,
 501                     "%s (%s) error log:" % (label, record["uuid"]), maxlen=40)
 502
 503             if record["output_uuid"]:
 504                 if self.arvrunner.trash_intermediate or self.arvrunner.intermediate_output_ttl:
 505                     # Compute the trash time to avoid requesting the collection record.
 506                     trash_at = ciso8601.parse_datetime_as_naive(record["modified_at"]) + datetime.timedelta(0, self.arvrunner.intermediate_output_ttl)
 507                     aftertime = " at %s" % trash_at.strftime("%Y-%m-%d %H:%M:%S UTC") if self.arvrunner.intermediate_output_ttl else ""
 508                     orpart = ", or" if self.arvrunner.trash_intermediate and self.arvrunner.intermediate_output_ttl else ""
 509                     oncomplete = " upon successful completion of the workflow" if self.arvrunner.trash_intermediate else ""
 510                     logger.info("%s Intermediate output %s (%s) will be trashed%s%s%s." % (
 511                         self.arvrunner.label(self), record["output_uuid"], container["output"], aftertime, orpart, oncomplete))
 512                 self.arvrunner.add_intermediate_output(record["output_uuid"])
 513
 514             if container["output"]:
 515                 outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
 516
 517             properties = record["properties"].copy()
 518             properties["cwl_output"] = outputs
 519             self.arvrunner.api.container_requests().update(
 520                 uuid=self.uuid,
 521                 body={"container_request": {"properties": properties}}
 522             ).execute(num_retries=self.arvrunner.num_retries)
 523         except WorkflowException as e:
 524             # Only include a stack trace if in debug mode.
 525             # A stack trace may obfuscate more useful output about the workflow.
 526             logger.error("%s unable to collect output from %s:\n%s",
 527                          self.arvrunner.label(self), container["output"], e, exc_info=(e if self.arvrunner.debug else False))
 528             processStatus = "permanentFail"
 529         except Exception:
 530             logger.exception("%s while getting output object:", self.arvrunner.label(self))
 531             processStatus = "permanentFail"
 532         finally:
 533             if not retried:
 534                 self.output_callback(outputs, processStatus)
 535
 536
 537 class RunnerContainer(Runner):
 538     """Submit and manage a container that runs arvados-cwl-runner."""
 539
 540     def arvados_job_spec(self, runtimeContext, git_info):
 541         """Create an Arvados container request for this workflow.
 542
 543         The returned dict can be used to create a container passed as
 544         the +body+ argument to container_requests().create().
 545         """
 546
 547         adjustDirObjs(self.job_order, trim_listing)
 548         visit_class(self.job_order, ("File", "Directory"), trim_anonymous_location)
 549         visit_class(self.job_order, ("File", "Directory"), remove_redundant_fields)
 550
 551         secret_mounts = {}
 552         for param in sorted(self.job_order.keys()):
 553             if self.secret_store.has_secret(self.job_order[param]):
 554                 mnt = "/secrets/s%d" % len(secret_mounts)
 555                 secret_mounts[mnt] = {
 556                     "kind": "text",
 557                     "content": self.secret_store.retrieve(self.job_order[param])
 558                 }
 559                 self.job_order[param] = {"$include": mnt}
 560
 561         container_req = {
 562             "name": self.name,
 563             "output_path": "/var/spool/cwl",
 564             "cwd": "/var/spool/cwl",
 565             "priority": self.priority,
 566             "state": "Committed",
 567             "container_image": arvados_jobs_image(self.arvrunner, self.jobs_image, runtimeContext),
 568             "mounts": {
 569                 "/var/lib/cwl/cwl.input.json": {
 570                     "kind": "json",
 571                     "content": self.job_order
 572                 },
 573                 "stdout": {
 574                     "kind": "file",
 575                     "path": "/var/spool/cwl/cwl.output.json"
 576                 },
 577                 "/var/spool/cwl": {
 578                     "kind": "collection",
 579                     "writable": True
 580                 }
 581             },
 582             "secret_mounts": secret_mounts,
 583             "runtime_constraints": {
 584                 "vcpus": math.ceil(self.submit_runner_cores),
 585                 "ram": 1024*1024 * (math.ceil(self.submit_runner_ram) + math.ceil(self.collection_cache_size)),
 586                 "API": True
 587             },
 588             "use_existing": False, # Never reuse the runner container - see #15497.
 589             "properties": {}
 590         }
 591
 592         if self.embedded_tool.tool.get("id", "").startswith("keep:"):
 593             sp = self.embedded_tool.tool["id"].split('/')
 594             workflowcollection = sp[0][5:]
 595             workflowname = "/".join(sp[1:])
 596             workflowpath = "/var/lib/cwl/workflow/%s" % workflowname
 597             container_req["mounts"]["/var/lib/cwl/workflow"] = {
 598                 "kind": "collection",
 599                 "portable_data_hash": "%s" % workflowcollection
 600             }
 601         elif self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
 602             uuid, frg = urllib.parse.urldefrag(self.embedded_tool.tool["id"])
 603             workflowpath = "/var/lib/cwl/workflow.json#" + frg
 604             packedtxt = self.loadingContext.loader.fetch_text(uuid)
 605             yaml = ruamel.yaml.YAML(typ='safe', pure=True)
 606             packed = yaml.load(packedtxt)
 607             container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
 608                 "kind": "json",
 609                 "content": packed
 610             }
 611             container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
 612         else:
 613             main = self.loadingContext.loader.idx["_:main"]
 614             if main.get("id") == "_:main":
 615                 del main["id"]
 616             workflowpath = "/var/lib/cwl/workflow.json#main"
 617             container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
 618                 "kind": "json",
 619                 "content": main
 620             }
 621
 622         container_req["properties"].update({k.replace("http://arvados.org/cwl#", "arv:"): v for k, v in git_info.items()})
 623
 624         properties_req, _ = self.embedded_tool.get_requirement("http://arvados.org/cwl#ProcessProperties")
 625         if properties_req:
 626             builder = make_builder(self.job_order, self.embedded_tool.hints, self.embedded_tool.requirements, runtimeContext, self.embedded_tool.metadata)
 627             for pr in properties_req["processProperties"]:
 628                 container_req["properties"][pr["propertyName"]] = builder.do_eval(pr["propertyValue"])
 629
 630         # --local means execute the workflow instead of submitting a container request
 631         # --api=containers means use the containers API
 632         # --no-log-timestamps means don't add timestamps (the logging infrastructure does this)
 633         # --disable-validate because we already validated so don't need to do it again
 634         # --eval-timeout is the timeout for javascript invocation
 635         # --parallel-task-count is the number of threads to use for job submission
 636         # --enable/disable-reuse sets desired job reuse
 637         # --collection-cache-size sets aside memory to store collections
 638         command = ["arvados-cwl-runner",
 639                    "--local",
 640                    "--api=containers",
 641                    "--no-log-timestamps",
 642                    "--disable-validate",
 643                    "--disable-color",
 644                    "--eval-timeout=%s" % self.arvrunner.eval_timeout,
 645                    "--thread-count=%s" % self.arvrunner.thread_count,
 646                    "--enable-reuse" if self.enable_reuse else "--disable-reuse",
 647                    "--collection-cache-size=%s" % self.collection_cache_size]
 648
 649         if self.output_name:
 650             command.append("--output-name=" + self.output_name)
 651             container_req["output_name"] = self.output_name
 652
 653         if self.output_tags:
 654             command.append("--output-tags=" + self.output_tags)
 655
 656         if runtimeContext.debug:
 657             command.append("--debug")
 658
 659         if runtimeContext.storage_classes != "default" and runtimeContext.storage_classes:
 660             command.append("--storage-classes=" + runtimeContext.storage_classes)
 661
 662         if runtimeContext.intermediate_storage_classes != "default" and runtimeContext.intermediate_storage_classes:
 663             command.append("--intermediate-storage-classes=" + runtimeContext.intermediate_storage_classes)
 664
 665         if runtimeContext.on_error:
 666             command.append("--on-error=" + self.on_error)
 667
 668         if runtimeContext.intermediate_output_ttl:
 669             command.append("--intermediate-output-ttl=%d" % runtimeContext.intermediate_output_ttl)
 670
 671         if runtimeContext.trash_intermediate:
 672             command.append("--trash-intermediate")
 673
 674         if runtimeContext.project_uuid:
 675             command.append("--project-uuid="+runtimeContext.project_uuid)
 676
 677         if self.enable_dev:
 678             command.append("--enable-dev")
 679
 680         if runtimeContext.enable_preemptible is True:
 681             command.append("--enable-preemptible")
 682
 683         if runtimeContext.enable_preemptible is False:
 684             command.append("--disable-preemptible")
 685
 686         if runtimeContext.varying_url_params:
 687             command.append("--varying-url-params="+runtimeContext.varying_url_params)
 688
 689         if runtimeContext.prefer_cached_downloads:
 690             command.append("--prefer-cached-downloads")
 691
 692         if self.fast_parser:
 693             command.append("--fast-parser")
 694
 695         command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
 696
 697         container_req["command"] = command
 698
 699         return container_req
 700
 701
 702     def run(self, runtimeContext):
 703         runtimeContext.keepprefix = "keep:"
 704         job_spec = self.arvados_job_spec(runtimeContext, self.git_info)
 705         if runtimeContext.project_uuid:
 706             job_spec["owner_uuid"] = runtimeContext.project_uuid
 707
 708         extra_submit_params = {}
 709         if runtimeContext.submit_runner_cluster:
 710             extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster
 711
 712         if runtimeContext.submit_request_uuid:
 713             if "cluster_id" in extra_submit_params:
 714                 # Doesn't make sense for "update" and actually fails
 715                 del extra_submit_params["cluster_id"]
 716             response = self.arvrunner.api.container_requests().update(
 717                 uuid=runtimeContext.submit_request_uuid,
 718                 body=job_spec,
 719                 **extra_submit_params
 720             ).execute(num_retries=self.arvrunner.num_retries)
 721         else:
 722             response = self.arvrunner.api.container_requests().create(
 723                 body=job_spec,
 724                 **extra_submit_params
 725             ).execute(num_retries=self.arvrunner.num_retries)
 726
 727         self.uuid = response["uuid"]
 728         self.arvrunner.process_submitted(self)
 729
 730         logger.info("%s submitted container_request %s", self.arvrunner.label(self), response["uuid"])
 731
 732         workbench1 = self.arvrunner.api.config()["Services"]["Workbench1"]["ExternalURL"]
 733         workbench2 = self.arvrunner.api.config()["Services"]["Workbench2"]["ExternalURL"]
 734         url = ""
 735         if workbench2:
 736             url = "{}processes/{}".format(workbench2, response["uuid"])
 737         elif workbench1:
 738             url = "{}container_requests/{}".format(workbench1, response["uuid"])
 739         if url:
 740             logger.info("Monitor workflow progress at %s", url)
 741
 742
 743     def done(self, record):
 744         try:
 745             container = self.arvrunner.api.containers().get(
 746                 uuid=record["container_uuid"]
 747             ).execute(num_retries=self.arvrunner.num_retries)
 748             container["log"] = record["log_uuid"]
 749         except Exception:
 750             logger.exception("%s while getting runner container", self.arvrunner.label(self))
 751             self.arvrunner.output_callback({}, "permanentFail")
 752         else:
 753             super(RunnerContainer, self).done(container)