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