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 import logging
   6 import json
   7 import os
   8 import urllib
   9 import time
  10 import datetime
  11 import ciso8601
  12 import uuid
  13
  14 from arvados_cwl.util import get_current_container, get_intermediate_collection_info
  15 import ruamel.yaml as yaml
  16
  17 from cwltool.errors import WorkflowException
  18 from cwltool.process import UnsupportedRequirement, shortname
  19 from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
  20 from cwltool.utils import aslist
  21 from cwltool.job import JobBase
  22
  23 import arvados.collection
  24
  25 from .arvdocker import arv_docker_get_image
  26 from . import done
  27 from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location, remove_redundant_fields
  28 from .fsaccess import CollectionFetcher
  29 from .pathmapper import NoFollowPathMapper, trim_listing
  30 from .perf import Perf
  31
  32 logger = logging.getLogger('arvados.cwl-runner')
  33 metrics = logging.getLogger('arvados.cwl-runner.metrics')
  34
  35 class ArvadosContainer(JobBase):
  36     """Submit and manage a Crunch container request for executing a CWL CommandLineTool."""
  37
  38     def __init__(self, runner,
  39                  builder,   # type: Builder
  40                  joborder,  # type: Dict[Text, Union[Dict[Text, Any], List, Text]]
  41                  make_path_mapper,  # type: Callable[..., PathMapper]
  42                  requirements,      # type: List[Dict[Text, Text]]
  43                  hints,     # type: List[Dict[Text, Text]]
  44                  name       # type: Text
  45     ):
  46         super(ArvadosContainer, self).__init__(builder, joborder, make_path_mapper, requirements, hints, name)
  47         self.arvrunner = runner
  48         self.running = False
  49         self.uuid = None
  50
  51     def update_pipeline_component(self, r):
  52         pass
  53
  54     def run(self, runtimeContext):
  55         # ArvadosCommandTool subclasses from cwltool.CommandLineTool,
  56         # which calls makeJobRunner() to get a new ArvadosContainer
  57         # object.  The fields that define execution such as
  58         # command_line, environment, etc are set on the
  59         # ArvadosContainer object by CommandLineTool.job() before
  60         # run() is called.
  61
  62         container_request = {
  63             "command": self.command_line,
  64             "name": self.name,
  65             "output_path": self.outdir,
  66             "cwd": self.outdir,
  67             "priority": runtimeContext.priority,
  68             "state": "Committed",
  69             "properties": {},
  70         }
  71         runtime_constraints = {}
  72
  73         if self.arvrunner.project_uuid:
  74             container_request["owner_uuid"] = self.arvrunner.project_uuid
  75
  76         if self.arvrunner.secret_store.has_secret(self.command_line):
  77             raise WorkflowException("Secret material leaked on command line, only file literals may contain secrets")
  78
  79         if self.arvrunner.secret_store.has_secret(self.environment):
  80             raise WorkflowException("Secret material leaked in environment, only file literals may contain secrets")
  81
  82         resources = self.builder.resources
  83         if resources is not None:
  84             runtime_constraints["vcpus"] = resources.get("cores", 1)
  85             runtime_constraints["ram"] = resources.get("ram") * 2**20
  86
  87         mounts = {
  88             self.outdir: {
  89                 "kind": "tmp",
  90                 "capacity": resources.get("outdirSize", 0) * 2**20
  91             },
  92             self.tmpdir: {
  93                 "kind": "tmp",
  94                 "capacity": resources.get("tmpdirSize", 0) * 2**20
  95             }
  96         }
  97         secret_mounts = {}
  98         scheduling_parameters = {}
  99
 100         rf = [self.pathmapper.mapper(f) for f in self.pathmapper.referenced_files]
 101         rf.sort(key=lambda k: k.resolved)
 102         prevdir = None
 103         for resolved, target, tp, stg in rf:
 104             if not stg:
 105                 continue
 106             if prevdir and target.startswith(prevdir):
 107                 continue
 108             if tp == "Directory":
 109                 targetdir = target
 110             else:
 111                 targetdir = os.path.dirname(target)
 112             sp = resolved.split("/", 1)
 113             pdh = sp[0][5:]   # remove "keep:"
 114             mounts[targetdir] = {
 115                 "kind": "collection",
 116                 "portable_data_hash": pdh
 117             }
 118             if len(sp) == 2:
 119                 if tp == "Directory":
 120                     path = sp[1]
 121                 else:
 122                     path = os.path.dirname(sp[1])
 123                 if path and path != "/":
 124                     mounts[targetdir]["path"] = path
 125             prevdir = targetdir + "/"
 126
 127         with Perf(metrics, "generatefiles %s" % self.name):
 128             if self.generatefiles["listing"]:
 129                 vwd = arvados.collection.Collection(api_client=self.arvrunner.api,
 130                                                     keep_client=self.arvrunner.keep_client,
 131                                                     num_retries=self.arvrunner.num_retries)
 132                 generatemapper = NoFollowPathMapper([self.generatefiles], "", "",
 133                                                     separateDirs=False)
 134
 135                 sorteditems = sorted(generatemapper.items(), None, key=lambda n: n[1].target)
 136
 137                 logger.debug("generatemapper is %s", sorteditems)
 138
 139                 with Perf(metrics, "createfiles %s" % self.name):
 140                     for f, p in sorteditems:
 141                         if not p.target:
 142                             pass
 143                         elif p.type in ("File", "Directory", "WritableFile", "WritableDirectory"):
 144                             if p.resolved.startswith("_:"):
 145                                 vwd.mkdirs(p.target)
 146                             else:
 147                                 source, path = self.arvrunner.fs_access.get_collection(p.resolved)
 148                                 vwd.copy(path, p.target, source_collection=source)
 149                         elif p.type == "CreateFile":
 150                             if self.arvrunner.secret_store.has_secret(p.resolved):
 151                                 secret_mounts["%s/%s" % (self.outdir, p.target)] = {
 152                                     "kind": "text",
 153                                     "content": self.arvrunner.secret_store.retrieve(p.resolved)
 154                                 }
 155                             else:
 156                                 with vwd.open(p.target, "w") as n:
 157                                     n.write(p.resolved.encode("utf-8"))
 158
 159                 def keepemptydirs(p):
 160                     if isinstance(p, arvados.collection.RichCollectionBase):
 161                         if len(p) == 0:
 162                             p.open(".keep", "w").close()
 163                         else:
 164                             for c in p:
 165                                 keepemptydirs(p[c])
 166
 167                 keepemptydirs(vwd)
 168
 169                 if not runtimeContext.current_container:
 170                     runtimeContext.current_container = get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger)
 171                 info = get_intermediate_collection_info(self.name, runtimeContext.current_container, runtimeContext.intermediate_output_ttl)
 172                 vwd.save_new(name=info["name"],
 173                              owner_uuid=self.arvrunner.project_uuid,
 174                              ensure_unique_name=True,
 175                              trash_at=info["trash_at"],
 176                              properties=info["properties"])
 177
 178                 prev = None
 179                 for f, p in sorteditems:
 180                     if (not p.target or self.arvrunner.secret_store.has_secret(p.resolved) or
 181                         (prev is not None and p.target.startswith(prev))):
 182                         continue
 183                     mountpoint = "%s/%s" % (self.outdir, p.target)
 184                     mounts[mountpoint] = {"kind": "collection",
 185                                           "portable_data_hash": vwd.portable_data_hash(),
 186                                           "path": p.target}
 187                     if p.type.startswith("Writable"):
 188                         mounts[mountpoint]["writable"] = True
 189                     prev = p.target + "/"
 190
 191         container_request["environment"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
 192         if self.environment:
 193             container_request["environment"].update(self.environment)
 194
 195         if self.stdin:
 196             sp = self.stdin[6:].split("/", 1)
 197             mounts["stdin"] = {"kind": "collection",
 198                                 "portable_data_hash": sp[0],
 199                                 "path": sp[1]}
 200
 201         if self.stderr:
 202             mounts["stderr"] = {"kind": "file",
 203                                 "path": "%s/%s" % (self.outdir, self.stderr)}
 204
 205         if self.stdout:
 206             mounts["stdout"] = {"kind": "file",
 207                                 "path": "%s/%s" % (self.outdir, self.stdout)}
 208
 209         (docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
 210         if not docker_req:
 211             docker_req = {"dockerImageId": "arvados/jobs"}
 212
 213         container_request["container_image"] = arv_docker_get_image(self.arvrunner.api,
 214                                                                      docker_req,
 215                                                                      runtimeContext.pull_image,
 216                                                                      self.arvrunner.project_uuid)
 217
 218         api_req, _ = self.get_requirement("http://arvados.org/cwl#APIRequirement")
 219         if api_req:
 220             runtime_constraints["API"] = True
 221
 222         runtime_req, _ = self.get_requirement("http://arvados.org/cwl#RuntimeConstraints")
 223         if runtime_req:
 224             if "keep_cache" in runtime_req:
 225                 runtime_constraints["keep_cache_ram"] = runtime_req["keep_cache"] * 2**20
 226             if "outputDirType" in runtime_req:
 227                 if runtime_req["outputDirType"] == "local_output_dir":
 228                     # Currently the default behavior.
 229                     pass
 230                 elif runtime_req["outputDirType"] == "keep_output_dir":
 231                     mounts[self.outdir]= {
 232                         "kind": "collection",
 233                         "writable": True
 234                     }
 235
 236         partition_req, _ = self.get_requirement("http://arvados.org/cwl#PartitionRequirement")
 237         if partition_req:
 238             scheduling_parameters["partitions"] = aslist(partition_req["partition"])
 239
 240         intermediate_output_req, _ = self.get_requirement("http://arvados.org/cwl#IntermediateOutput")
 241         if intermediate_output_req:
 242             self.output_ttl = intermediate_output_req["outputTTL"]
 243         else:
 244             self.output_ttl = self.arvrunner.intermediate_output_ttl
 245
 246         if self.output_ttl < 0:
 247             raise WorkflowException("Invalid value %d for output_ttl, cannot be less than zero" % container_request["output_ttl"])
 248
 249         if self.timelimit is not None:
 250             scheduling_parameters["max_run_time"] = self.timelimit
 251
 252         container_request["output_name"] = "Output for step %s" % (self.name)
 253         container_request["output_ttl"] = self.output_ttl
 254         container_request["mounts"] = mounts
 255         container_request["secret_mounts"] = secret_mounts
 256         container_request["runtime_constraints"] = runtime_constraints
 257         container_request["scheduling_parameters"] = scheduling_parameters
 258
 259         enable_reuse = runtimeContext.enable_reuse
 260         if enable_reuse:
 261             reuse_req, _ = self.get_requirement("http://arvados.org/cwl#ReuseRequirement")
 262             if reuse_req:
 263                 enable_reuse = reuse_req["enableReuse"]
 264         container_request["use_existing"] = enable_reuse
 265
 266         if runtimeContext.runnerjob.startswith("arvwf:"):
 267             wfuuid = runtimeContext.runnerjob[6:runtimeContext.runnerjob.index("#")]
 268             wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(num_retries=self.arvrunner.num_retries)
 269             if container_request["name"] == "main":
 270                 container_request["name"] = wfrecord["name"]
 271             container_request["properties"]["template_uuid"] = wfuuid
 272
 273         self.output_callback = self.arvrunner.get_wrapped_callback(self.output_callback)
 274
 275         try:
 276             if runtimeContext.submit_request_uuid:
 277                 response = self.arvrunner.api.container_requests().update(
 278                     uuid=runtimeContext.submit_request_uuid,
 279                     body=container_request
 280                 ).execute(num_retries=self.arvrunner.num_retries)
 281             else:
 282                 response = self.arvrunner.api.container_requests().create(
 283                     body=container_request
 284                 ).execute(num_retries=self.arvrunner.num_retries)
 285
 286             self.uuid = response["uuid"]
 287             self.arvrunner.process_submitted(self)
 288
 289             if response["state"] == "Final":
 290                 logger.info("%s reused container %s", self.arvrunner.label(self), response["container_uuid"])
 291             else:
 292                 logger.info("%s %s state is %s", self.arvrunner.label(self), response["uuid"], response["state"])
 293         except Exception as e:
 294             logger.error("%s got error %s" % (self.arvrunner.label(self), str(e)))
 295             self.output_callback({}, "permanentFail")
 296
 297     def done(self, record):
 298         outputs = {}
 299         try:
 300             container = self.arvrunner.api.containers().get(
 301                 uuid=record["container_uuid"]
 302             ).execute(num_retries=self.arvrunner.num_retries)
 303             if container["state"] == "Complete":
 304                 rcode = container["exit_code"]
 305                 if self.successCodes and rcode in self.successCodes:
 306                     processStatus = "success"
 307                 elif self.temporaryFailCodes and rcode in self.temporaryFailCodes:
 308                     processStatus = "temporaryFail"
 309                 elif self.permanentFailCodes and rcode in self.permanentFailCodes:
 310                     processStatus = "permanentFail"
 311                 elif rcode == 0:
 312                     processStatus = "success"
 313                 else:
 314                     processStatus = "permanentFail"
 315             else:
 316                 processStatus = "permanentFail"
 317
 318             if processStatus == "permanentFail":
 319                 logc = arvados.collection.CollectionReader(container["log"],
 320                                                            api_client=self.arvrunner.api,
 321                                                            keep_client=self.arvrunner.keep_client,
 322                                                            num_retries=self.arvrunner.num_retries)
 323                 done.logtail(logc, logger.error, "%s (%s) error log:" % (self.arvrunner.label(self), record["uuid"]), maxlen=40)
 324
 325             if record["output_uuid"]:
 326                 if self.arvrunner.trash_intermediate or self.arvrunner.intermediate_output_ttl:
 327                     # Compute the trash time to avoid requesting the collection record.
 328                     trash_at = ciso8601.parse_datetime_unaware(record["modified_at"]) + datetime.timedelta(0, self.arvrunner.intermediate_output_ttl)
 329                     aftertime = " at %s" % trash_at.strftime("%Y-%m-%d %H:%M:%S UTC") if self.arvrunner.intermediate_output_ttl else ""
 330                     orpart = ", or" if self.arvrunner.trash_intermediate and self.arvrunner.intermediate_output_ttl else ""
 331                     oncomplete = " upon successful completion of the workflow" if self.arvrunner.trash_intermediate else ""
 332                     logger.info("%s Intermediate output %s (%s) will be trashed%s%s%s." % (
 333                         self.arvrunner.label(self), record["output_uuid"], container["output"], aftertime, orpart, oncomplete))
 334                 self.arvrunner.add_intermediate_output(record["output_uuid"])
 335
 336             if container["output"]:
 337                 outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
 338         except WorkflowException as e:
 339             logger.error("%s unable to collect output from %s:\n%s",
 340                          self.arvrunner.label(self), container["output"], e, exc_info=(e if self.arvrunner.debug else False))
 341             processStatus = "permanentFail"
 342         except Exception as e:
 343             logger.exception("%s while getting output object: %s", self.arvrunner.label(self), e)
 344             processStatus = "permanentFail"
 345         finally:
 346             self.output_callback(outputs, processStatus)
 347
 348
 349 class RunnerContainer(Runner):
 350     """Submit and manage a container that runs arvados-cwl-runner."""
 351
 352     def arvados_job_spec(self, runtimeContext):
 353         """Create an Arvados container request for this workflow.
 354
 355         The returned dict can be used to create a container passed as
 356         the +body+ argument to container_requests().create().
 357         """
 358
 359         adjustDirObjs(self.job_order, trim_listing)
 360         visit_class(self.job_order, ("File", "Directory"), trim_anonymous_location)
 361         visit_class(self.job_order, ("File", "Directory"), remove_redundant_fields)
 362
 363         secret_mounts = {}
 364         for param in sorted(self.job_order.keys()):
 365             if self.secret_store.has_secret(self.job_order[param]):
 366                 mnt = "/secrets/s%d" % len(secret_mounts)
 367                 secret_mounts[mnt] = {
 368                     "kind": "text",
 369                     "content": self.secret_store.retrieve(self.job_order[param])
 370                 }
 371                 self.job_order[param] = {"$include": mnt}
 372
 373         container_req = {
 374             "name": self.name,
 375             "output_path": "/var/spool/cwl",
 376             "cwd": "/var/spool/cwl",
 377             "priority": self.priority,
 378             "state": "Committed",
 379             "container_image": arvados_jobs_image(self.arvrunner, self.jobs_image),
 380             "mounts": {
 381                 "/var/lib/cwl/cwl.input.json": {
 382                     "kind": "json",
 383                     "content": self.job_order
 384                 },
 385                 "stdout": {
 386                     "kind": "file",
 387                     "path": "/var/spool/cwl/cwl.output.json"
 388                 },
 389                 "/var/spool/cwl": {
 390                     "kind": "collection",
 391                     "writable": True
 392                 }
 393             },
 394             "secret_mounts": secret_mounts,
 395             "runtime_constraints": {
 396                 "vcpus": self.submit_runner_cores,
 397                 "ram": 1024*1024 * self.submit_runner_ram,
 398                 "API": True
 399             },
 400             "use_existing": self.enable_reuse,
 401             "properties": {}
 402         }
 403
 404         if self.tool.tool.get("id", "").startswith("keep:"):
 405             sp = self.tool.tool["id"].split('/')
 406             workflowcollection = sp[0][5:]
 407             workflowname = "/".join(sp[1:])
 408             workflowpath = "/var/lib/cwl/workflow/%s" % workflowname
 409             container_req["mounts"]["/var/lib/cwl/workflow"] = {
 410                 "kind": "collection",
 411                 "portable_data_hash": "%s" % workflowcollection
 412             }
 413         else:
 414             packed = packed_workflow(self.arvrunner, self.tool, self.merged_map)
 415             workflowpath = "/var/lib/cwl/workflow.json#main"
 416             container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
 417                 "kind": "json",
 418                 "content": packed
 419             }
 420             if self.tool.tool.get("id", "").startswith("arvwf:"):
 421                 container_req["properties"]["template_uuid"] = self.tool.tool["id"][6:33]
 422
 423
 424         # --local means execute the workflow instead of submitting a container request
 425         # --api=containers means use the containers API
 426         # --no-log-timestamps means don't add timestamps (the logging infrastructure does this)
 427         # --disable-validate because we already validated so don't need to do it again
 428         # --eval-timeout is the timeout for javascript invocation
 429         # --parallel-task-count is the number of threads to use for job submission
 430         # --enable/disable-reuse sets desired job reuse
 431         command = ["arvados-cwl-runner",
 432                    "--local",
 433                    "--api=containers",
 434                    "--no-log-timestamps",
 435                    "--disable-validate",
 436                    "--eval-timeout=%s" % self.arvrunner.eval_timeout,
 437                    "--thread-count=%s" % self.arvrunner.thread_count,
 438                    "--enable-reuse" if self.enable_reuse else "--disable-reuse"]
 439
 440         if self.output_name:
 441             command.append("--output-name=" + self.output_name)
 442             container_req["output_name"] = self.output_name
 443
 444         if self.output_tags:
 445             command.append("--output-tags=" + self.output_tags)
 446
 447         if runtimeContext.debug:
 448             command.append("--debug")
 449
 450         if runtimeContext.storage_classes != "default":
 451             command.append("--storage-classes=" + runtimeContext.storage_classes)
 452
 453         if self.on_error:
 454             command.append("--on-error=" + self.on_error)
 455
 456         if self.intermediate_output_ttl:
 457             command.append("--intermediate-output-ttl=%d" % self.intermediate_output_ttl)
 458
 459         if self.arvrunner.trash_intermediate:
 460             command.append("--trash-intermediate")
 461
 462         if self.arvrunner.project_uuid:
 463             command.append("--project-uuid="+self.arvrunner.project_uuid)
 464
 465         command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
 466
 467         container_req["command"] = command
 468
 469         return container_req
 470
 471
 472     def run(self, runtimeContext):
 473         runtimeContext.keepprefix = "keep:"
 474         job_spec = self.arvados_job_spec(runtimeContext)
 475         if self.arvrunner.project_uuid:
 476             job_spec["owner_uuid"] = self.arvrunner.project_uuid
 477
 478         if runtimeContext.submit_request_uuid:
 479             response = self.arvrunner.api.container_requests().update(
 480                 uuid=runtimeContext.submit_request_uuid,
 481                 body=job_spec
 482             ).execute(num_retries=self.arvrunner.num_retries)
 483         else:
 484             response = self.arvrunner.api.container_requests().create(
 485                 body=job_spec
 486             ).execute(num_retries=self.arvrunner.num_retries)
 487
 488         self.uuid = response["uuid"]
 489         self.arvrunner.process_submitted(self)
 490
 491         logger.info("%s submitted container_request %s", self.arvrunner.label(self), response["uuid"])
 492
 493     def done(self, record):
 494         try:
 495             container = self.arvrunner.api.containers().get(
 496                 uuid=record["container_uuid"]
 497             ).execute(num_retries=self.arvrunner.num_retries)
 498         except Exception as e:
 499             logger.exception("%s while getting runner container: %s", self.arvrunner.label(self), e)
 500             self.arvrunner.output_callback({}, "permanentFail")
 501         else:
 502             super(RunnerContainer, self).done(container)