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         ram_multiplier = [1]
 371
 372         oom_retry_req, _ = self.get_requirement("http://arvados.org/cwl#OutOfMemoryRetry")
 373         if oom_retry_req:
 374             if oom_retry_req.get('memoryRetryMultiplier'):
 375                 ram_multiplier.append(oom_retry_req.get('memoryRetryMultiplier'))
 376             elif oom_retry_req.get('memoryRetryMultipler'):
 377                 ram_multiplier.append(oom_retry_req.get('memoryRetryMultipler'))
 378
 379         if runtimeContext.runnerjob.startswith("arvwf:"):
 380             wfuuid = runtimeContext.runnerjob[6:runtimeContext.runnerjob.index("#")]
 381             wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(num_retries=self.arvrunner.num_retries)
 382             if container_request["name"] == "main":
 383                 container_request["name"] = wfrecord["name"]
 384             container_request["properties"]["template_uuid"] = wfuuid
 385
 386         if self.attempt_count == 0:
 387             self.output_callback = self.arvrunner.get_wrapped_callback(self.output_callback)
 388
 389         try:
 390             ram = runtime_constraints["ram"]
 391
 392             self.uuid = runtimeContext.submit_request_uuid
 393
 394             for i in ram_multiplier:
 395                 runtime_constraints["ram"] = ram * i
 396
 397                 if self.uuid:
 398                     response = self.arvrunner.api.container_requests().update(
 399                         uuid=self.uuid,
 400                         body=container_request,
 401                         **extra_submit_params
 402                     ).execute(num_retries=self.arvrunner.num_retries)
 403                 else:
 404                     response = self.arvrunner.api.container_requests().create(
 405                         body=container_request,
 406                         **extra_submit_params
 407                     ).execute(num_retries=self.arvrunner.num_retries)
 408                     self.uuid = response["uuid"]
 409
 410                 if response["container_uuid"] is not None:
 411                     break
 412
 413             if response["container_uuid"] is None:
 414                 runtime_constraints["ram"] = ram * ram_multiplier[self.attempt_count]
 415
 416             container_request["state"] = "Committed"
 417             response = self.arvrunner.api.container_requests().update(
 418                 uuid=self.uuid,
 419                 body=container_request,
 420                 **extra_submit_params
 421             ).execute(num_retries=self.arvrunner.num_retries)
 422
 423             self.arvrunner.process_submitted(self)
 424             self.attempt_count += 1
 425
 426             if response["state"] == "Final":
 427                 logger.info("%s reused container %s", self.arvrunner.label(self), response["container_uuid"])
 428             else:
 429                 logger.info("%s %s state is %s", self.arvrunner.label(self), response["uuid"], response["state"])
 430         except Exception as e:
 431             logger.exception("%s error submitting container\n%s", self.arvrunner.label(self), e)
 432             logger.debug("Container request was %s", container_request)
 433             self.output_callback({}, "permanentFail")
 434
 435     def out_of_memory_retry(self, record, container):
 436         oom_retry_req, _ = self.get_requirement("http://arvados.org/cwl#OutOfMemoryRetry")
 437         if oom_retry_req is None:
 438             return False
 439
 440         # Sometimes it gets killed with no warning
 441         if container["exit_code"] == 137:
 442             return True
 443
 444         logc = arvados.collection.CollectionReader(record["log_uuid"],
 445                                                    api_client=self.arvrunner.api,
 446                                                    keep_client=self.arvrunner.keep_client,
 447                                                    num_retries=self.arvrunner.num_retries)
 448
 449         loglines = [""]
 450         def callback(v1, v2, v3):
 451             loglines[0] = v3
 452
 453         done.logtail(logc, callback, "", maxlen=1000)
 454
 455         # Check allocation failure
 456         oom_matches = oom_retry_req.get('memoryErrorRegex') or r'(bad_alloc|out ?of ?memory|memory ?error|container using over 9.% of memory)'
 457         if re.search(oom_matches, loglines[0], re.IGNORECASE | re.MULTILINE):
 458             return True
 459
 460         return False
 461
 462     def done(self, record):
 463         outputs = {}
 464         retried = False
 465         rcode = None
 466         try:
 467             container = self.arvrunner.api.containers().get(
 468                 uuid=record["container_uuid"]
 469             ).execute(num_retries=self.arvrunner.num_retries)
 470             if container["state"] == "Complete":
 471                 rcode = container["exit_code"]
 472                 if self.successCodes and rcode in self.successCodes:
 473                     processStatus = "success"
 474                 elif self.temporaryFailCodes and rcode in self.temporaryFailCodes:
 475                     processStatus = "temporaryFail"
 476                 elif self.permanentFailCodes and rcode in self.permanentFailCodes:
 477                     processStatus = "permanentFail"
 478                 elif rcode == 0:
 479                     processStatus = "success"
 480                 else:
 481                     processStatus = "permanentFail"
 482
 483                 if processStatus == "permanentFail" and self.attempt_count == 1 and self.out_of_memory_retry(record, container):
 484                     logger.warning("%s Container failed with out of memory error, retrying with more RAM.",
 485                                  self.arvrunner.label(self))
 486                     self.job_runtime.submit_request_uuid = None
 487                     self.uuid = None
 488                     self.run(None)
 489                     retried = True
 490                     return
 491
 492                 if rcode == 137:
 493                     logger.warning("%s Container may have been killed for using too much RAM.  Try resubmitting with a higher 'ramMin' or use the arv:OutOfMemoryRetry feature.",
 494                                  self.arvrunner.label(self))
 495             else:
 496                 processStatus = "permanentFail"
 497
 498             if processStatus == "permanentFail" and record["log_uuid"]:
 499                 logc = arvados.collection.CollectionReader(record["log_uuid"],
 500                                                            api_client=self.arvrunner.api,
 501                                                            keep_client=self.arvrunner.keep_client,
 502                                                            num_retries=self.arvrunner.num_retries)
 503                 label = self.arvrunner.label(self)
 504                 done.logtail(
 505                     logc, logger.error,
 506                     "%s (%s) error log:" % (label, record["uuid"]), maxlen=40, include_crunchrun=(rcode is None or rcode > 127))
 507
 508             if record["output_uuid"]:
 509                 if self.arvrunner.trash_intermediate or self.arvrunner.intermediate_output_ttl:
 510                     # Compute the trash time to avoid requesting the collection record.
 511                     trash_at = ciso8601.parse_datetime_as_naive(record["modified_at"]) + datetime.timedelta(0, self.arvrunner.intermediate_output_ttl)
 512                     aftertime = " at %s" % trash_at.strftime("%Y-%m-%d %H:%M:%S UTC") if self.arvrunner.intermediate_output_ttl else ""
 513                     orpart = ", or" if self.arvrunner.trash_intermediate and self.arvrunner.intermediate_output_ttl else ""
 514                     oncomplete = " upon successful completion of the workflow" if self.arvrunner.trash_intermediate else ""
 515                     logger.info("%s Intermediate output %s (%s) will be trashed%s%s%s." % (
 516                         self.arvrunner.label(self), record["output_uuid"], container["output"], aftertime, orpart, oncomplete))
 517                 self.arvrunner.add_intermediate_output(record["output_uuid"])
 518
 519             if container["output"]:
 520                 outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
 521
 522             properties = record["properties"].copy()
 523             properties["cwl_output"] = outputs
 524             self.arvrunner.api.container_requests().update(
 525                 uuid=self.uuid,
 526                 body={"container_request": {"properties": properties}}
 527             ).execute(num_retries=self.arvrunner.num_retries)
 528         except WorkflowException as e:
 529             # Only include a stack trace if in debug mode.
 530             # A stack trace may obfuscate more useful output about the workflow.
 531             logger.error("%s unable to collect output from %s:\n%s",
 532                          self.arvrunner.label(self), container["output"], e, exc_info=(e if self.arvrunner.debug else False))
 533             processStatus = "permanentFail"
 534         except Exception:
 535             logger.exception("%s while getting output object:", self.arvrunner.label(self))
 536             processStatus = "permanentFail"
 537         finally:
 538             if not retried:
 539                 self.output_callback(outputs, processStatus)
 540
 541
 542 class RunnerContainer(Runner):
 543     """Submit and manage a container that runs arvados-cwl-runner."""
 544
 545     def arvados_job_spec(self, runtimeContext, git_info):
 546         """Create an Arvados container request for this workflow.
 547
 548         The returned dict can be used to create a container passed as
 549         the +body+ argument to container_requests().create().
 550         """
 551
 552         adjustDirObjs(self.job_order, trim_listing)
 553         visit_class(self.job_order, ("File", "Directory"), trim_anonymous_location)
 554         visit_class(self.job_order, ("File", "Directory"), remove_redundant_fields)
 555
 556         secret_mounts = {}
 557         for param in sorted(self.job_order.keys()):
 558             if self.secret_store.has_secret(self.job_order[param]):
 559                 mnt = "/secrets/s%d" % len(secret_mounts)
 560                 secret_mounts[mnt] = {
 561                     "kind": "text",
 562                     "content": self.secret_store.retrieve(self.job_order[param])
 563                 }
 564                 self.job_order[param] = {"$include": mnt}
 565
 566         container_image = arvados_jobs_image(self.arvrunner, self.jobs_image, runtimeContext)
 567
 568         workflow_runner_req, _ = self.embedded_tool.get_requirement("http://arvados.org/cwl#WorkflowRunnerResources")
 569         if workflow_runner_req and workflow_runner_req.get("acrContainerImage"):
 570             container_image = workflow_runner_req.get("acrContainerImage")
 571
 572         container_req = {
 573             "name": self.name,
 574             "output_path": "/var/spool/cwl",
 575             "cwd": "/var/spool/cwl",
 576             "priority": self.priority,
 577             "state": "Committed",
 578             "container_image": container_image,
 579             "mounts": {
 580                 "/var/lib/cwl/cwl.input.json": {
 581                     "kind": "json",
 582                     "content": self.job_order
 583                 },
 584                 "stdout": {
 585                     "kind": "file",
 586                     "path": "/var/spool/cwl/cwl.output.json"
 587                 },
 588                 "/var/spool/cwl": {
 589                     "kind": "collection",
 590                     "writable": True
 591                 }
 592             },
 593             "secret_mounts": secret_mounts,
 594             "runtime_constraints": {
 595                 "vcpus": math.ceil(self.submit_runner_cores),
 596                 "ram": 1024*1024 * (math.ceil(self.submit_runner_ram) + math.ceil(self.collection_cache_size)),
 597                 "API": True
 598             },
 599             "use_existing": self.reuse_runner,
 600             "properties": {}
 601         }
 602
 603         if self.embedded_tool.tool.get("id", "").startswith("keep:"):
 604             sp = self.embedded_tool.tool["id"].split('/')
 605             workflowcollection = sp[0][5:]
 606             workflowname = "/".join(sp[1:])
 607             workflowpath = "/var/lib/cwl/workflow/%s" % workflowname
 608             container_req["mounts"]["/var/lib/cwl/workflow"] = {
 609                 "kind": "collection",
 610                 "portable_data_hash": "%s" % workflowcollection
 611             }
 612         elif self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
 613             uuid, frg = urllib.parse.urldefrag(self.embedded_tool.tool["id"])
 614             workflowpath = "/var/lib/cwl/workflow.json#" + frg
 615             packedtxt = self.loadingContext.loader.fetch_text(uuid)
 616             yaml = ruamel.yaml.YAML(typ='safe', pure=True)
 617             packed = yaml.load(packedtxt)
 618             container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
 619                 "kind": "json",
 620                 "content": packed
 621             }
 622             container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
 623         elif self.embedded_tool.tool.get("id", "").startswith("file:"):
 624             raise WorkflowException("Tool id '%s' is a local file but expected keep: or arvwf:" % self.embedded_tool.tool.get("id"))
 625         else:
 626             main = self.loadingContext.loader.idx["_:main"]
 627             if main.get("id") == "_:main":
 628                 del main["id"]
 629             workflowpath = "/var/lib/cwl/workflow.json#main"
 630             container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
 631                 "kind": "json",
 632                 "content": main
 633             }
 634
 635         container_req["properties"].update({k.replace("http://arvados.org/cwl#", "arv:"): v for k, v in git_info.items()})
 636
 637         properties_req, _ = self.embedded_tool.get_requirement("http://arvados.org/cwl#ProcessProperties")
 638         if properties_req:
 639             builder = make_builder(self.job_order, self.embedded_tool.hints, self.embedded_tool.requirements, runtimeContext, self.embedded_tool.metadata)
 640             for pr in properties_req["processProperties"]:
 641                 container_req["properties"][pr["propertyName"]] = builder.do_eval(pr["propertyValue"])
 642
 643         # --local means execute the workflow instead of submitting a container request
 644         # --api=containers means use the containers API
 645         # --no-log-timestamps means don't add timestamps (the logging infrastructure does this)
 646         # --disable-validate because we already validated so don't need to do it again
 647         # --eval-timeout is the timeout for javascript invocation
 648         # --parallel-task-count is the number of threads to use for job submission
 649         # --enable/disable-reuse sets desired job reuse
 650         # --collection-cache-size sets aside memory to store collections
 651         command = ["arvados-cwl-runner",
 652                    "--local",
 653                    "--api=containers",
 654                    "--no-log-timestamps",
 655                    "--disable-validate",
 656                    "--disable-color",
 657                    "--eval-timeout=%s" % self.arvrunner.eval_timeout,
 658                    "--thread-count=%s" % self.arvrunner.thread_count,
 659                    "--enable-reuse" if self.enable_reuse else "--disable-reuse",
 660                    "--collection-cache-size=%s" % self.collection_cache_size]
 661
 662         if self.output_name:
 663             command.append("--output-name=" + self.output_name)
 664             container_req["output_name"] = self.output_name
 665
 666         if self.output_tags:
 667             command.append("--output-tags=" + self.output_tags)
 668
 669         if runtimeContext.debug:
 670             command.append("--debug")
 671
 672         if runtimeContext.storage_classes != "default" and runtimeContext.storage_classes:
 673             command.append("--storage-classes=" + runtimeContext.storage_classes)
 674
 675         if runtimeContext.intermediate_storage_classes != "default" and runtimeContext.intermediate_storage_classes:
 676             command.append("--intermediate-storage-classes=" + runtimeContext.intermediate_storage_classes)
 677
 678         if runtimeContext.on_error:
 679             command.append("--on-error=" + self.on_error)
 680
 681         if runtimeContext.intermediate_output_ttl:
 682             command.append("--intermediate-output-ttl=%d" % runtimeContext.intermediate_output_ttl)
 683
 684         if runtimeContext.trash_intermediate:
 685             command.append("--trash-intermediate")
 686
 687         if runtimeContext.project_uuid:
 688             command.append("--project-uuid="+runtimeContext.project_uuid)
 689
 690         if self.enable_dev:
 691             command.append("--enable-dev")
 692
 693         if runtimeContext.enable_preemptible is True:
 694             command.append("--enable-preemptible")
 695
 696         if runtimeContext.enable_preemptible is False:
 697             command.append("--disable-preemptible")
 698
 699         if runtimeContext.varying_url_params:
 700             command.append("--varying-url-params="+runtimeContext.varying_url_params)
 701
 702         if runtimeContext.prefer_cached_downloads:
 703             command.append("--prefer-cached-downloads")
 704
 705         if self.fast_parser:
 706             command.append("--fast-parser")
 707
 708         command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
 709
 710         container_req["command"] = command
 711
 712         return container_req
 713
 714
 715     def run(self, runtimeContext):
 716         runtimeContext.keepprefix = "keep:"
 717         job_spec = self.arvados_job_spec(runtimeContext, self.git_info)
 718         if runtimeContext.project_uuid:
 719             job_spec["owner_uuid"] = runtimeContext.project_uuid
 720
 721         extra_submit_params = {}
 722         if runtimeContext.submit_runner_cluster:
 723             extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster
 724
 725         if runtimeContext.submit_request_uuid:
 726             if "cluster_id" in extra_submit_params:
 727                 # Doesn't make sense for "update" and actually fails
 728                 del extra_submit_params["cluster_id"]
 729             response = self.arvrunner.api.container_requests().update(
 730                 uuid=runtimeContext.submit_request_uuid,
 731                 body=job_spec,
 732                 **extra_submit_params
 733             ).execute(num_retries=self.arvrunner.num_retries)
 734         else:
 735             response = self.arvrunner.api.container_requests().create(
 736                 body=job_spec,
 737                 **extra_submit_params
 738             ).execute(num_retries=self.arvrunner.num_retries)
 739
 740         self.uuid = response["uuid"]
 741         self.arvrunner.process_submitted(self)
 742
 743         logger.info("%s submitted container_request %s", self.arvrunner.label(self), response["uuid"])
 744
 745         workbench2 = self.arvrunner.api.config()["Services"]["Workbench2"]["ExternalURL"]
 746         if workbench2:
 747             url = "{}processes/{}".format(workbench2, response["uuid"])
 748             logger.info("Monitor workflow progress at %s", url)
 749
 750
 751     def done(self, record):
 752         try:
 753             container = self.arvrunner.api.containers().get(
 754                 uuid=record["container_uuid"]
 755             ).execute(num_retries=self.arvrunner.num_retries)
 756             container["log"] = record["log_uuid"]
 757         except Exception:
 758             logger.exception("%s while getting runner container", self.arvrunner.label(self))
 759             self.arvrunner.output_callback({}, "permanentFail")
 760         else:
 761             super(RunnerContainer, self).done(container)