sdk/cwl/arvados_cwl/__init__.py

   1 #!/usr/bin/env python
   2 # Copyright (C) The Arvados Authors. All rights reserved.
   3 #
   4 # SPDX-License-Identifier: Apache-2.0
   5
   6 # Implement cwl-runner interface for submitting and running work on Arvados, using
   7 # either the Crunch jobs API or Crunch containers API.
   8
   9 import argparse
  10 import logging
  11 import os
  12 import sys
  13 import threading
  14 import hashlib
  15 import copy
  16 import json
  17 import re
  18 from functools import partial
  19 import pkg_resources  # part of setuptools
  20 import Queue
  21 import time
  22 import signal
  23 import thread
  24
  25 from cwltool.errors import WorkflowException
  26 import cwltool.main
  27 import cwltool.workflow
  28 import cwltool.process
  29 from schema_salad.sourceline import SourceLine
  30 import schema_salad.validate as validate
  31 import cwltool.argparser
  32
  33 import arvados
  34 import arvados.config
  35 from arvados.keep import KeepClient
  36 from arvados.errors import ApiError
  37 import arvados.commands._util as arv_cmd
  38
  39 from .arvcontainer import ArvadosContainer, RunnerContainer
  40 from .arvjob import ArvadosJob, RunnerJob, RunnerTemplate
  41 from. runner import Runner, upload_docker, upload_job_order, upload_workflow_deps
  42 from .arvtool import ArvadosCommandTool
  43 from .arvworkflow import ArvadosWorkflow, upload_workflow
  44 from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver, CollectionCache
  45 from .perf import Perf
  46 from .pathmapper import NoFollowPathMapper
  47 from .task_queue import TaskQueue
  48 from .context import ArvLoadingContext, ArvRuntimeContext
  49 from ._version import __version__
  50
  51 from cwltool.pack import pack
  52 from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema
  53 from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, get_listing
  54 from cwltool.command_line_tool import compute_checksums
  55
  56 from arvados.api import OrderedJsonModel
  57
  58 logger = logging.getLogger('arvados.cwl-runner')
  59 metrics = logging.getLogger('arvados.cwl-runner.metrics')
  60 logger.setLevel(logging.INFO)
  61
  62 arvados.log_handler.setFormatter(logging.Formatter(
  63         '%(asctime)s %(name)s %(levelname)s: %(message)s',
  64         '%Y-%m-%d %H:%M:%S'))
  65
  66 DEFAULT_PRIORITY = 500
  67
  68 class ArvCwlRunner(object):
  69     """Execute a CWL tool or workflow, submit work (using either jobs or
  70     containers API), wait for them to complete, and report output.
  71
  72     """
  73
  74     def __init__(self, api_client,
  75                  arvargs=None,
  76                  keep_client=None,
  77                  num_retries=4,
  78                  thread_count=4):
  79
  80         if arvargs is None:
  81             arvargs = argparse.Namespace()
  82             arvargs.work_api = None
  83             arvargs.output_name = None
  84             arvargs.output_tags = None
  85             arvargs.thread_count = 1
  86
  87         self.api = api_client
  88         self.processes = {}
  89         self.workflow_eval_lock = threading.Condition(threading.RLock())
  90         self.final_output = None
  91         self.final_status = None
  92         self.num_retries = num_retries
  93         self.uuid = None
  94         self.stop_polling = threading.Event()
  95         self.poll_api = None
  96         self.pipeline = None
  97         self.final_output_collection = None
  98         self.output_name = arvargs.output_name
  99         self.output_tags = arvargs.output_tags
 100         self.project_uuid = None
 101         self.intermediate_output_ttl = 0
 102         self.intermediate_output_collections = []
 103         self.trash_intermediate = False
 104         self.thread_count = arvargs.thread_count
 105         self.poll_interval = 12
 106         self.loadingContext = None
 107
 108         if keep_client is not None:
 109             self.keep_client = keep_client
 110         else:
 111             self.keep_client = arvados.keep.KeepClient(api_client=self.api, num_retries=self.num_retries)
 112
 113         self.collection_cache = CollectionCache(self.api, self.keep_client, self.num_retries)
 114
 115         self.fetcher_constructor = partial(CollectionFetcher,
 116                                            api_client=self.api,
 117                                            fs_access=CollectionFsAccess("", collection_cache=self.collection_cache),
 118                                            num_retries=self.num_retries)
 119
 120         self.work_api = None
 121         expected_api = ["jobs", "containers"]
 122         for api in expected_api:
 123             try:
 124                 methods = self.api._rootDesc.get('resources')[api]['methods']
 125                 if ('httpMethod' in methods['create'] and
 126                     (arvargs.work_api == api or arvargs.work_api is None)):
 127                     self.work_api = api
 128                     break
 129             except KeyError:
 130                 pass
 131
 132         if not self.work_api:
 133             if arvargs.work_api is None:
 134                 raise Exception("No supported APIs")
 135             else:
 136                 raise Exception("Unsupported API '%s', expected one of %s" % (work_api, expected_api))
 137
 138         if self.work_api == "jobs":
 139             logger.warn("""
 140 *******************************
 141 Using the deprecated 'jobs' API.
 142
 143 To get rid of this warning:
 144
 145 Users: read about migrating at
 146 http://doc.arvados.org/user/cwl/cwl-style.html#migrate
 147 and use the option --api=containers
 148
 149 Admins: configure the cluster to disable the 'jobs' API as described at:
 150 http://doc.arvados.org/install/install-api-server.html#disable_api_methods
 151 *******************************""")
 152
 153         self.loadingContext = ArvLoadingContext(vars(arvargs))
 154         self.loadingContext.fetcher_constructor = self.fetcher_constructor
 155         self.loadingContext.resolver = partial(collectionResolver, self.api, num_retries=self.num_retries)
 156         self.loadingContext.construct_tool_object = self.arv_make_tool
 157
 158
 159     def arv_make_tool(self, toolpath_object, loadingContext):
 160         if "class" in toolpath_object and toolpath_object["class"] == "CommandLineTool":
 161             return ArvadosCommandTool(self, toolpath_object, loadingContext)
 162         elif "class" in toolpath_object and toolpath_object["class"] == "Workflow":
 163             return ArvadosWorkflow(self, toolpath_object, loadingContext)
 164         else:
 165             return cwltool.workflow.default_make_tool(toolpath_object, loadingContext)
 166
 167     def output_callback(self, out, processStatus):
 168         with self.workflow_eval_lock:
 169             if processStatus == "success":
 170                 logger.info("Overall process status is %s", processStatus)
 171                 if self.pipeline:
 172                     self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
 173                                                          body={"state": "Complete"}).execute(num_retries=self.num_retries)
 174             else:
 175                 logger.error("Overall process status is %s", processStatus)
 176                 if self.pipeline:
 177                     self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
 178                                                          body={"state": "Failed"}).execute(num_retries=self.num_retries)
 179             self.final_status = processStatus
 180             self.final_output = out
 181             self.workflow_eval_lock.notifyAll()
 182
 183
 184     def start_run(self, runnable, runtimeContext):
 185         self.task_queue.add(partial(runnable.run, runtimeContext))
 186
 187     def process_submitted(self, container):
 188         with self.workflow_eval_lock:
 189             self.processes[container.uuid] = container
 190
 191     def process_done(self, uuid, record):
 192         with self.workflow_eval_lock:
 193             j = self.processes[uuid]
 194             logger.info("%s %s is %s", self.label(j), uuid, record["state"])
 195             self.task_queue.add(partial(j.done, record))
 196             del self.processes[uuid]
 197
 198     def wrapped_callback(self, cb, obj, st):
 199         with self.workflow_eval_lock:
 200             cb(obj, st)
 201             self.workflow_eval_lock.notifyAll()
 202
 203     def get_wrapped_callback(self, cb):
 204         return partial(self.wrapped_callback, cb)
 205
 206     def on_message(self, event):
 207         if event.get("object_uuid") in self.processes and event["event_type"] == "update":
 208             uuid = event["object_uuid"]
 209             if event["properties"]["new_attributes"]["state"] == "Running":
 210                 with self.workflow_eval_lock:
 211                     j = self.processes[uuid]
 212                     if j.running is False:
 213                         j.running = True
 214                         j.update_pipeline_component(event["properties"]["new_attributes"])
 215                         logger.info("%s %s is Running", self.label(j), uuid)
 216             elif event["properties"]["new_attributes"]["state"] in ("Complete", "Failed", "Cancelled", "Final"):
 217                 self.process_done(uuid, event["properties"]["new_attributes"])
 218
 219     def label(self, obj):
 220         return "[%s %s]" % (self.work_api[0:-1], obj.name)
 221
 222     def poll_states(self):
 223         """Poll status of jobs or containers listed in the processes dict.
 224
 225         Runs in a separate thread.
 226         """
 227
 228         try:
 229             remain_wait = self.poll_interval
 230             while True:
 231                 if remain_wait > 0:
 232                     self.stop_polling.wait(remain_wait)
 233                 if self.stop_polling.is_set():
 234                     break
 235                 with self.workflow_eval_lock:
 236                     keys = list(self.processes.keys())
 237                 if not keys:
 238                     remain_wait = self.poll_interval
 239                     continue
 240
 241                 begin_poll = time.time()
 242                 if self.work_api == "containers":
 243                     table = self.poll_api.container_requests()
 244                 elif self.work_api == "jobs":
 245                     table = self.poll_api.jobs()
 246
 247                 try:
 248                     proc_states = table.list(filters=[["uuid", "in", keys]]).execute(num_retries=self.num_retries)
 249                 except Exception as e:
 250                     logger.warn("Error checking states on API server: %s", e)
 251                     remain_wait = self.poll_interval
 252                     continue
 253
 254                 for p in proc_states["items"]:
 255                     self.on_message({
 256                         "object_uuid": p["uuid"],
 257                         "event_type": "update",
 258                         "properties": {
 259                             "new_attributes": p
 260                         }
 261                     })
 262                 finish_poll = time.time()
 263                 remain_wait = self.poll_interval - (finish_poll - begin_poll)
 264         except:
 265             logger.exception("Fatal error in state polling thread.")
 266             with self.workflow_eval_lock:
 267                 self.processes.clear()
 268                 self.workflow_eval_lock.notifyAll()
 269         finally:
 270             self.stop_polling.set()
 271
 272     def add_intermediate_output(self, uuid):
 273         if uuid:
 274             self.intermediate_output_collections.append(uuid)
 275
 276     def trash_intermediate_output(self):
 277         logger.info("Cleaning up intermediate output collections")
 278         for i in self.intermediate_output_collections:
 279             try:
 280                 self.api.collections().delete(uuid=i).execute(num_retries=self.num_retries)
 281             except:
 282                 logger.warn("Failed to delete intermediate output: %s", sys.exc_info()[1], exc_info=(sys.exc_info()[1] if self.debug else False))
 283             if sys.exc_info()[0] is KeyboardInterrupt or sys.exc_info()[0] is SystemExit:
 284                 break
 285
 286     def check_features(self, obj):
 287         if isinstance(obj, dict):
 288             if obj.get("writable") and self.work_api != "containers":
 289                 raise SourceLine(obj, "writable", UnsupportedRequirement).makeError("InitialWorkDir feature 'writable: true' not supported with --api=jobs")
 290             if obj.get("class") == "DockerRequirement":
 291                 if obj.get("dockerOutputDirectory"):
 292                     if self.work_api != "containers":
 293                         raise SourceLine(obj, "dockerOutputDirectory", UnsupportedRequirement).makeError(
 294                             "Option 'dockerOutputDirectory' of DockerRequirement not supported with --api=jobs.")
 295                     if not obj.get("dockerOutputDirectory").startswith('/'):
 296                         raise SourceLine(obj, "dockerOutputDirectory", validate.ValidationException).makeError(
 297                             "Option 'dockerOutputDirectory' must be an absolute path.")
 298             if obj.get("class") == "http://commonwl.org/cwltool#Secrets" and self.work_api != "containers":
 299                 raise SourceLine(obj, "class", UnsupportedRequirement).makeError("Secrets not supported with --api=jobs")
 300             for v in obj.itervalues():
 301                 self.check_features(v)
 302         elif isinstance(obj, list):
 303             for i,v in enumerate(obj):
 304                 with SourceLine(obj, i, UnsupportedRequirement, logger.isEnabledFor(logging.DEBUG)):
 305                     self.check_features(v)
 306
 307     def make_output_collection(self, name, storage_classes, tagsString, outputObj):
 308         outputObj = copy.deepcopy(outputObj)
 309
 310         files = []
 311         def capture(fileobj):
 312             files.append(fileobj)
 313
 314         adjustDirObjs(outputObj, capture)
 315         adjustFileObjs(outputObj, capture)
 316
 317         generatemapper = NoFollowPathMapper(files, "", "", separateDirs=False)
 318
 319         final = arvados.collection.Collection(api_client=self.api,
 320                                               keep_client=self.keep_client,
 321                                               num_retries=self.num_retries)
 322
 323         for k,v in generatemapper.items():
 324             if k.startswith("_:"):
 325                 if v.type == "Directory":
 326                     continue
 327                 if v.type == "CreateFile":
 328                     with final.open(v.target, "wb") as f:
 329                         f.write(v.resolved.encode("utf-8"))
 330                     continue
 331
 332             if not k.startswith("keep:"):
 333                 raise Exception("Output source is not in keep or a literal")
 334             sp = k.split("/")
 335             srccollection = sp[0][5:]
 336             try:
 337                 reader = self.collection_cache.get(srccollection)
 338                 srcpath = "/".join(sp[1:]) if len(sp) > 1 else "."
 339                 final.copy(srcpath, v.target, source_collection=reader, overwrite=False)
 340             except arvados.errors.ArgumentError as e:
 341                 logger.error("Creating CollectionReader for '%s' '%s': %s", k, v, e)
 342                 raise
 343             except IOError as e:
 344                 logger.warn("While preparing output collection: %s", e)
 345
 346         def rewrite(fileobj):
 347             fileobj["location"] = generatemapper.mapper(fileobj["location"]).target
 348             for k in ("listing", "contents", "nameext", "nameroot", "dirname"):
 349                 if k in fileobj:
 350                     del fileobj[k]
 351
 352         adjustDirObjs(outputObj, rewrite)
 353         adjustFileObjs(outputObj, rewrite)
 354
 355         with final.open("cwl.output.json", "w") as f:
 356             json.dump(outputObj, f, sort_keys=True, indent=4, separators=(',',': '))
 357
 358         final.save_new(name=name, owner_uuid=self.project_uuid, storage_classes=storage_classes, ensure_unique_name=True)
 359
 360         logger.info("Final output collection %s \"%s\" (%s)", final.portable_data_hash(),
 361                     final.api_response()["name"],
 362                     final.manifest_locator())
 363
 364         final_uuid = final.manifest_locator()
 365         tags = tagsString.split(',')
 366         for tag in tags:
 367              self.api.links().create(body={
 368                 "head_uuid": final_uuid, "link_class": "tag", "name": tag
 369                 }).execute(num_retries=self.num_retries)
 370
 371         def finalcollection(fileobj):
 372             fileobj["location"] = "keep:%s/%s" % (final.portable_data_hash(), fileobj["location"])
 373
 374         adjustDirObjs(outputObj, finalcollection)
 375         adjustFileObjs(outputObj, finalcollection)
 376
 377         return (outputObj, final)
 378
 379     def set_crunch_output(self):
 380         if self.work_api == "containers":
 381             try:
 382                 current = self.api.containers().current().execute(num_retries=self.num_retries)
 383             except ApiError as e:
 384                 # Status code 404 just means we're not running in a container.
 385                 if e.resp.status != 404:
 386                     logger.info("Getting current container: %s", e)
 387                 return
 388             try:
 389                 self.api.containers().update(uuid=current['uuid'],
 390                                              body={
 391                                                  'output': self.final_output_collection.portable_data_hash(),
 392                                              }).execute(num_retries=self.num_retries)
 393                 self.api.collections().update(uuid=self.final_output_collection.manifest_locator(),
 394                                               body={
 395                                                   'is_trashed': True
 396                                               }).execute(num_retries=self.num_retries)
 397             except Exception as e:
 398                 logger.info("Setting container output: %s", e)
 399         elif self.work_api == "jobs" and "TASK_UUID" in os.environ:
 400             self.api.job_tasks().update(uuid=os.environ["TASK_UUID"],
 401                                    body={
 402                                        'output': self.final_output_collection.portable_data_hash(),
 403                                        'success': self.final_status == "success",
 404                                        'progress':1.0
 405                                    }).execute(num_retries=self.num_retries)
 406
 407     def arv_executor(self, tool, job_order, runtimeContext, logger=None):
 408         self.debug = runtimeContext.debug
 409
 410         tool.visit(self.check_features)
 411
 412         self.project_uuid = runtimeContext.project_uuid
 413         self.pipeline = None
 414         self.fs_access = runtimeContext.make_fs_access(runtimeContext.basedir)
 415         self.secret_store = runtimeContext.secret_store
 416
 417         self.trash_intermediate = runtimeContext.trash_intermediate
 418         if self.trash_intermediate and self.work_api != "containers":
 419             raise Exception("--trash-intermediate is only supported with --api=containers.")
 420
 421         self.intermediate_output_ttl = runtimeContext.intermediate_output_ttl
 422         if self.intermediate_output_ttl and self.work_api != "containers":
 423             raise Exception("--intermediate-output-ttl is only supported with --api=containers.")
 424         if self.intermediate_output_ttl < 0:
 425             raise Exception("Invalid value %d for --intermediate-output-ttl, cannot be less than zero" % self.intermediate_output_ttl)
 426
 427         if runtimeContext.submit_request_uuid and self.work_api != "containers":
 428             raise Exception("--submit-request-uuid requires containers API, but using '{}' api".format(self.work_api))
 429
 430         if not runtimeContext.name:
 431             runtimeContext.name = self.name = tool.tool.get("label") or tool.metadata.get("label") or os.path.basename(tool.tool["id"])
 432
 433         # Upload direct dependencies of workflow steps, get back mapping of files to keep references.
 434         # Also uploads docker images.
 435         merged_map = upload_workflow_deps(self, tool)
 436
 437         # Reload tool object which may have been updated by
 438         # upload_workflow_deps
 439         # Don't validate this time because it will just print redundant errors.
 440         loadingContext = self.loadingContext.copy()
 441         loadingContext.loader = tool.doc_loader
 442         loadingContext.avsc_names = tool.doc_schema
 443         loadingContext.metadata = tool.metadata
 444         loadingContext.do_validate = False
 445
 446         tool = self.arv_make_tool(tool.doc_loader.idx[tool.tool["id"]],
 447                                   loadingContext)
 448
 449         # Upload local file references in the job order.
 450         job_order = upload_job_order(self, "%s input" % runtimeContext.name,
 451                                      tool, job_order)
 452
 453         existing_uuid = runtimeContext.update_workflow
 454         if existing_uuid or runtimeContext.create_workflow:
 455             # Create a pipeline template or workflow record and exit.
 456             if self.work_api == "jobs":
 457                 tmpl = RunnerTemplate(self, tool, job_order,
 458                                       runtimeContext.enable_reuse,
 459                                       uuid=existing_uuid,
 460                                       submit_runner_ram=runtimeContext.submit_runner_ram,
 461                                       name=runtimeContext.name,
 462                                       merged_map=merged_map)
 463                 tmpl.save()
 464                 # cwltool.main will write our return value to stdout.
 465                 return (tmpl.uuid, "success")
 466             elif self.work_api == "containers":
 467                 return (upload_workflow(self, tool, job_order,
 468                                         self.project_uuid,
 469                                         uuid=existing_uuid,
 470                                         submit_runner_ram=runtimeContext.submit_runner_ram,
 471                                         name=runtimeContext.name,
 472                                         merged_map=merged_map),
 473                         "success")
 474
 475         self.ignore_docker_for_reuse = runtimeContext.ignore_docker_for_reuse
 476         self.eval_timeout = runtimeContext.eval_timeout
 477
 478         runtimeContext = runtimeContext.copy()
 479         runtimeContext.use_container = True
 480         runtimeContext.tmpdir_prefix = "tmp"
 481         runtimeContext.work_api = self.work_api
 482
 483         if self.work_api == "containers":
 484             if self.ignore_docker_for_reuse:
 485                 raise Exception("--ignore-docker-for-reuse not supported with containers API.")
 486             runtimeContext.outdir = "/var/spool/cwl"
 487             runtimeContext.docker_outdir = "/var/spool/cwl"
 488             runtimeContext.tmpdir = "/tmp"
 489             runtimeContext.docker_tmpdir = "/tmp"
 490         elif self.work_api == "jobs":
 491             if runtimeContext.priority != DEFAULT_PRIORITY:
 492                 raise Exception("--priority not implemented for jobs API.")
 493             runtimeContext.outdir = "$(task.outdir)"
 494             runtimeContext.docker_outdir = "$(task.outdir)"
 495             runtimeContext.tmpdir = "$(task.tmpdir)"
 496
 497         if runtimeContext.priority < 1 or runtimeContext.priority > 1000:
 498             raise Exception("--priority must be in the range 1..1000.")
 499
 500         runnerjob = None
 501         if runtimeContext.submit:
 502             # Submit a runner job to run the workflow for us.
 503             if self.work_api == "containers":
 504                 if tool.tool["class"] == "CommandLineTool" and runtimeContext.wait:
 505                     runtimeContext.runnerjob = tool.tool["id"]
 506                     runnerjob = tool.job(job_order,
 507                                          self.output_callback,
 508                                          runtimeContext).next()
 509                 else:
 510                     runnerjob = RunnerContainer(self, tool, job_order, runtimeContext.enable_reuse,
 511                                                 self.output_name,
 512                                                 self.output_tags,
 513                                                 submit_runner_ram=runtimeContext.submit_runner_ram,
 514                                                 name=runtimeContext.name,
 515                                                 on_error=runtimeContext.on_error,
 516                                                 submit_runner_image=runtimeContext.submit_runner_image,
 517                                                 intermediate_output_ttl=runtimeContext.intermediate_output_ttl,
 518                                                 merged_map=merged_map,
 519                                                 priority=runtimeContext.priority,
 520                                                 secret_store=self.secret_store)
 521             elif self.work_api == "jobs":
 522                 runnerjob = RunnerJob(self, tool, job_order, runtimeContext.enable_reuse,
 523                                       self.output_name,
 524                                       self.output_tags,
 525                                       submit_runner_ram=runtimeContext.submit_runner_ram,
 526                                       name=runtimeContext.name,
 527                                       on_error=runtimeContext.on_error,
 528                                       submit_runner_image=runtimeContext.submit_runner_image,
 529                                       merged_map=merged_map)
 530         elif runtimeContext.cwl_runner_job is None and self.work_api == "jobs":
 531             # Create pipeline for local run
 532             self.pipeline = self.api.pipeline_instances().create(
 533                 body={
 534                     "owner_uuid": self.project_uuid,
 535                     "name": runtimeContext.name if runtimeContext.name else shortname(tool.tool["id"]),
 536                     "components": {},
 537                     "state": "RunningOnClient"}).execute(num_retries=self.num_retries)
 538             logger.info("Pipeline instance %s", self.pipeline["uuid"])
 539
 540         if runnerjob and not runtimeContext.wait:
 541             submitargs = runtimeContext.copy()
 542             submitargs.submit = False
 543             runnerjob.run(submitargs)
 544             return (runnerjob.uuid, "success")
 545
 546         self.poll_api = arvados.api('v1')
 547         self.polling_thread = threading.Thread(target=self.poll_states)
 548         self.polling_thread.start()
 549
 550         self.task_queue = TaskQueue(self.workflow_eval_lock, self.thread_count)
 551
 552         if runnerjob:
 553             jobiter = iter((runnerjob,))
 554         else:
 555             if runtimeContext.cwl_runner_job is not None:
 556                 self.uuid = runtimeContext.cwl_runner_job.get('uuid')
 557             jobiter = tool.job(job_order,
 558                                self.output_callback,
 559                                runtimeContext)
 560
 561         try:
 562             self.workflow_eval_lock.acquire()
 563             # Holds the lock while this code runs and releases it when
 564             # it is safe to do so in self.workflow_eval_lock.wait(),
 565             # at which point on_message can update job state and
 566             # process output callbacks.
 567
 568             loopperf = Perf(metrics, "jobiter")
 569             loopperf.__enter__()
 570             for runnable in jobiter:
 571                 loopperf.__exit__()
 572
 573                 if self.stop_polling.is_set():
 574                     break
 575
 576                 if self.task_queue.error is not None:
 577                     raise self.task_queue.error
 578
 579                 if runnable:
 580                     with Perf(metrics, "run"):
 581                         self.start_run(runnable, runtimeContext)
 582                 else:
 583                     if (self.task_queue.in_flight + len(self.processes)) > 0:
 584                         self.workflow_eval_lock.wait(3)
 585                     else:
 586                         logger.error("Workflow is deadlocked, no runnable processes and not waiting on any pending processes.")
 587                         break
 588                 loopperf.__enter__()
 589             loopperf.__exit__()
 590
 591             while (self.task_queue.in_flight + len(self.processes)) > 0:
 592                 if self.task_queue.error is not None:
 593                     raise self.task_queue.error
 594                 self.workflow_eval_lock.wait(3)
 595
 596         except UnsupportedRequirement:
 597             raise
 598         except:
 599             if sys.exc_info()[0] is KeyboardInterrupt or sys.exc_info()[0] is SystemExit:
 600                 logger.error("Interrupted, workflow will be cancelled")
 601             else:
 602                 logger.error("Execution failed: %s", sys.exc_info()[1], exc_info=(sys.exc_info()[1] if self.debug else False))
 603             if self.pipeline:
 604                 self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
 605                                                      body={"state": "Failed"}).execute(num_retries=self.num_retries)
 606             if runnerjob and runnerjob.uuid and self.work_api == "containers":
 607                 self.api.container_requests().update(uuid=runnerjob.uuid,
 608                                                      body={"priority": "0"}).execute(num_retries=self.num_retries)
 609         finally:
 610             self.workflow_eval_lock.release()
 611             self.task_queue.drain()
 612             self.stop_polling.set()
 613             self.polling_thread.join()
 614             self.task_queue.join()
 615
 616         if self.final_status == "UnsupportedRequirement":
 617             raise UnsupportedRequirement("Check log for details.")
 618
 619         if self.final_output is None:
 620             raise WorkflowException("Workflow did not return a result.")
 621
 622         if runtimeContext.submit and isinstance(runnerjob, Runner):
 623             logger.info("Final output collection %s", runnerjob.final_output)
 624         else:
 625             if self.output_name is None:
 626                 self.output_name = "Output of %s" % (shortname(tool.tool["id"]))
 627             if self.output_tags is None:
 628                 self.output_tags = ""
 629
 630             storage_classes = runtimeContext.storage_classes.strip().split(",")
 631             self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, storage_classes, self.output_tags, self.final_output)
 632             self.set_crunch_output()
 633
 634         if runtimeContext.compute_checksum:
 635             adjustDirObjs(self.final_output, partial(get_listing, self.fs_access))
 636             adjustFileObjs(self.final_output, partial(compute_checksums, self.fs_access))
 637
 638         if self.trash_intermediate and self.final_status == "success":
 639             self.trash_intermediate_output()
 640
 641         return (self.final_output, self.final_status)
 642
 643
 644 def versionstring():
 645     """Print version string of key packages for provenance and debugging."""
 646
 647     arvcwlpkg = pkg_resources.require("arvados-cwl-runner")
 648     arvpkg = pkg_resources.require("arvados-python-client")
 649     cwlpkg = pkg_resources.require("cwltool")
 650
 651     return "%s %s, %s %s, %s %s" % (sys.argv[0], arvcwlpkg[0].version,
 652                                     "arvados-python-client", arvpkg[0].version,
 653                                     "cwltool", cwlpkg[0].version)
 654
 655
 656 def arg_parser():  # type: () -> argparse.ArgumentParser
 657     parser = argparse.ArgumentParser(description='Arvados executor for Common Workflow Language')
 658
 659     parser.add_argument("--basedir", type=str,
 660                         help="Base directory used to resolve relative references in the input, default to directory of input object file or current directory (if inputs piped/provided on command line).")
 661     parser.add_argument("--outdir", type=str, default=os.path.abspath('.'),
 662                         help="Output directory, default current directory")
 663
 664     parser.add_argument("--eval-timeout",
 665                         help="Time to wait for a Javascript expression to evaluate before giving an error, default 20s.",
 666                         type=float,
 667                         default=20)
 668
 669     exgroup = parser.add_mutually_exclusive_group()
 670     exgroup.add_argument("--print-dot", action="store_true",
 671                          help="Print workflow visualization in graphviz format and exit")
 672     exgroup.add_argument("--version", action="version", help="Print version and exit", version=versionstring())
 673     exgroup.add_argument("--validate", action="store_true", help="Validate CWL document only.")
 674
 675     exgroup = parser.add_mutually_exclusive_group()
 676     exgroup.add_argument("--verbose", action="store_true", help="Default logging")
 677     exgroup.add_argument("--quiet", action="store_true", help="Only print warnings and errors.")
 678     exgroup.add_argument("--debug", action="store_true", help="Print even more logging")
 679
 680     parser.add_argument("--metrics", action="store_true", help="Print timing metrics")
 681
 682     parser.add_argument("--tool-help", action="store_true", help="Print command line help for tool")
 683
 684     exgroup = parser.add_mutually_exclusive_group()
 685     exgroup.add_argument("--enable-reuse", action="store_true",
 686                         default=True, dest="enable_reuse",
 687                         help="Enable job or container reuse (default)")
 688     exgroup.add_argument("--disable-reuse", action="store_false",
 689                         default=True, dest="enable_reuse",
 690                         help="Disable job or container reuse")
 691
 692     parser.add_argument("--project-uuid", type=str, metavar="UUID", help="Project that will own the workflow jobs, if not provided, will go to home project.")
 693     parser.add_argument("--output-name", type=str, help="Name to use for collection that stores the final output.", default=None)
 694     parser.add_argument("--output-tags", type=str, help="Tags for the final output collection separated by commas, e.g., '--output-tags tag0,tag1,tag2'.", default=None)
 695     parser.add_argument("--ignore-docker-for-reuse", action="store_true",
 696                         help="Ignore Docker image version when deciding whether to reuse past jobs.",
 697                         default=False)
 698
 699     exgroup = parser.add_mutually_exclusive_group()
 700     exgroup.add_argument("--submit", action="store_true", help="Submit workflow to run on Arvados.",
 701                         default=True, dest="submit")
 702     exgroup.add_argument("--local", action="store_false", help="Run workflow on local host (submits jobs to Arvados).",
 703                         default=True, dest="submit")
 704     exgroup.add_argument("--create-template", action="store_true", help="(Deprecated) synonym for --create-workflow.",
 705                          dest="create_workflow")
 706     exgroup.add_argument("--create-workflow", action="store_true", help="Create an Arvados workflow (if using the 'containers' API) or pipeline template (if using the 'jobs' API). See --api.")
 707     exgroup.add_argument("--update-workflow", type=str, metavar="UUID", help="Update an existing Arvados workflow or pipeline template with the given UUID.")
 708
 709     exgroup = parser.add_mutually_exclusive_group()
 710     exgroup.add_argument("--wait", action="store_true", help="After submitting workflow runner job, wait for completion.",
 711                         default=True, dest="wait")
 712     exgroup.add_argument("--no-wait", action="store_false", help="Submit workflow runner job and exit.",
 713                         default=True, dest="wait")
 714
 715     exgroup = parser.add_mutually_exclusive_group()
 716     exgroup.add_argument("--log-timestamps", action="store_true", help="Prefix logging lines with timestamp",
 717                         default=True, dest="log_timestamps")
 718     exgroup.add_argument("--no-log-timestamps", action="store_false", help="No timestamp on logging lines",
 719                         default=True, dest="log_timestamps")
 720
 721     parser.add_argument("--api", type=str,
 722                         default=None, dest="work_api",
 723                         choices=("jobs", "containers"),
 724                         help="Select work submission API.  Default is 'jobs' if that API is available, otherwise 'containers'.")
 725
 726     parser.add_argument("--compute-checksum", action="store_true", default=False,
 727                         help="Compute checksum of contents while collecting outputs",
 728                         dest="compute_checksum")
 729
 730     parser.add_argument("--submit-runner-ram", type=int,
 731                         help="RAM (in MiB) required for the workflow runner job (default 1024)",
 732                         default=None)
 733
 734     parser.add_argument("--submit-runner-image", type=str,
 735                         help="Docker image for workflow runner job, default arvados/jobs:%s" % __version__,
 736                         default=None)
 737
 738     parser.add_argument("--submit-request-uuid", type=str,
 739                         default=None,
 740                         help="Update and commit supplied container request instead of creating a new one (containers API only).")
 741
 742     parser.add_argument("--name", type=str,
 743                         help="Name to use for workflow execution instance.",
 744                         default=None)
 745
 746     parser.add_argument("--on-error", type=str,
 747                         help="Desired workflow behavior when a step fails.  One of 'stop' or 'continue'. "
 748                         "Default is 'continue'.", default="continue", choices=("stop", "continue"))
 749
 750     parser.add_argument("--enable-dev", action="store_true",
 751                         help="Enable loading and running development versions "
 752                              "of CWL spec.", default=False)
 753     parser.add_argument('--storage-classes', default="default", type=str,
 754                         help="Specify comma separated list of storage classes to be used when saving workflow output to Keep.")
 755
 756     parser.add_argument("--intermediate-output-ttl", type=int, metavar="N",
 757                         help="If N > 0, intermediate output collections will be trashed N seconds after creation.  Default is 0 (don't trash).",
 758                         default=0)
 759
 760     parser.add_argument("--priority", type=int,
 761                         help="Workflow priority (range 1..1000, higher has precedence over lower, containers api only)",
 762                         default=DEFAULT_PRIORITY)
 763
 764     parser.add_argument("--disable-validate", dest="do_validate",
 765                         action="store_false", default=True,
 766                         help=argparse.SUPPRESS)
 767
 768     parser.add_argument("--disable-js-validation",
 769                         action="store_true", default=False,
 770                         help=argparse.SUPPRESS)
 771
 772     parser.add_argument("--thread-count", type=int,
 773                         default=4, help="Number of threads to use for job submit and output collection.")
 774
 775     exgroup = parser.add_mutually_exclusive_group()
 776     exgroup.add_argument("--trash-intermediate", action="store_true",
 777                         default=False, dest="trash_intermediate",
 778                          help="Immediately trash intermediate outputs on workflow success.")
 779     exgroup.add_argument("--no-trash-intermediate", action="store_false",
 780                         default=False, dest="trash_intermediate",
 781                         help="Do not trash intermediate outputs (default).")
 782
 783     parser.add_argument("workflow", type=str, default=None, help="The workflow to execute")
 784     parser.add_argument("job_order", nargs=argparse.REMAINDER, help="The input object to the workflow.")
 785
 786     return parser
 787
 788 def add_arv_hints():
 789     cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*")
 790     cwltool.command_line_tool.ACCEPTLIST_RE = cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE
 791     res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml')
 792     use_custom_schema("v1.0", "http://arvados.org/cwl", res.read())
 793     res.close()
 794     cwltool.process.supportedProcessRequirements.extend([
 795         "http://arvados.org/cwl#RunInSingleContainer",
 796         "http://arvados.org/cwl#OutputDirType",
 797         "http://arvados.org/cwl#RuntimeConstraints",
 798         "http://arvados.org/cwl#PartitionRequirement",
 799         "http://arvados.org/cwl#APIRequirement",
 800         "http://commonwl.org/cwltool#LoadListingRequirement",
 801         "http://arvados.org/cwl#IntermediateOutput",
 802         "http://arvados.org/cwl#ReuseRequirement"
 803     ])
 804
 805 def exit_signal_handler(sigcode, frame):
 806     logger.error("Caught signal {}, exiting.".format(sigcode))
 807     sys.exit(-sigcode)
 808
 809 def main(args, stdout, stderr, api_client=None, keep_client=None,
 810          install_sig_handlers=True):
 811     parser = arg_parser()
 812
 813     job_order_object = None
 814     arvargs = parser.parse_args(args)
 815
 816     if len(arvargs.storage_classes.strip().split(',')) > 1:
 817         logger.error("Multiple storage classes are not supported currently.")
 818         return 1
 819
 820     arvargs.use_container = True
 821     arvargs.relax_path_checks = True
 822     arvargs.print_supported_versions = False
 823
 824     if install_sig_handlers:
 825         arv_cmd.install_signal_handlers()
 826
 827     if arvargs.update_workflow:
 828         if arvargs.update_workflow.find('-7fd4e-') == 5:
 829             want_api = 'containers'
 830         elif arvargs.update_workflow.find('-p5p6p-') == 5:
 831             want_api = 'jobs'
 832         else:
 833             want_api = None
 834         if want_api and arvargs.work_api and want_api != arvargs.work_api:
 835             logger.error('--update-workflow arg {!r} uses {!r} API, but --api={!r} specified'.format(
 836                 arvargs.update_workflow, want_api, arvargs.work_api))
 837             return 1
 838         arvargs.work_api = want_api
 839
 840     if (arvargs.create_workflow or arvargs.update_workflow) and not arvargs.job_order:
 841         job_order_object = ({}, "")
 842
 843     add_arv_hints()
 844
 845     try:
 846         if api_client is None:
 847             api_client = arvados.safeapi.ThreadSafeApiCache(api_params={"model": OrderedJsonModel()}, keep_params={"num_retries": 4})
 848             keep_client = api_client.keep
 849             # Make an API object now so errors are reported early.
 850             api_client.users().current().execute()
 851         if keep_client is None:
 852             keep_client = arvados.keep.KeepClient(api_client=api_client, num_retries=4)
 853         runner = ArvCwlRunner(api_client, arvargs, keep_client=keep_client, num_retries=4)
 854     except Exception as e:
 855         logger.error(e)
 856         return 1
 857
 858     if arvargs.debug:
 859         logger.setLevel(logging.DEBUG)
 860         logging.getLogger('arvados').setLevel(logging.DEBUG)
 861
 862     if arvargs.quiet:
 863         logger.setLevel(logging.WARN)
 864         logging.getLogger('arvados').setLevel(logging.WARN)
 865         logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
 866
 867     if arvargs.metrics:
 868         metrics.setLevel(logging.DEBUG)
 869         logging.getLogger("cwltool.metrics").setLevel(logging.DEBUG)
 870
 871     if arvargs.log_timestamps:
 872         arvados.log_handler.setFormatter(logging.Formatter(
 873             '%(asctime)s %(name)s %(levelname)s: %(message)s',
 874             '%Y-%m-%d %H:%M:%S'))
 875     else:
 876         arvados.log_handler.setFormatter(logging.Formatter('%(name)s %(levelname)s: %(message)s'))
 877
 878     for key, val in cwltool.argparser.get_default_args().items():
 879         if not hasattr(arvargs, key):
 880             setattr(arvargs, key, val)
 881
 882     runtimeContext = ArvRuntimeContext(vars(arvargs))
 883     runtimeContext.make_fs_access = partial(CollectionFsAccess,
 884                              collection_cache=runner.collection_cache)
 885
 886     return cwltool.main.main(args=arvargs,
 887                              stdout=stdout,
 888                              stderr=stderr,
 889                              executor=runner.arv_executor,
 890                              versionfunc=versionstring,
 891                              job_order_object=job_order_object,
 892                              logger_handler=arvados.log_handler,
 893                              custom_schema_callback=add_arv_hints,
 894                              loadingContext=runner.loadingContext,
 895                              runtimeContext=runtimeContext)