sdk/cwl/arvados_cwl/__init__.py

   1 #!/usr/bin/env python
   2
   3 # Implement cwl-runner interface for submitting and running work on Arvados, using
   4 # either the Crunch jobs API or Crunch containers API.
   5
   6 import argparse
   7 import logging
   8 import os
   9 import sys
  10 import threading
  11 import hashlib
  12 import copy
  13 import json
  14 from functools import partial
  15 import pkg_resources  # part of setuptools
  16
  17 from cwltool.errors import WorkflowException
  18 import cwltool.main
  19 import cwltool.workflow
  20 import schema_salad
  21
  22 import arvados
  23 import arvados.config
  24
  25 from .arvcontainer import ArvadosContainer, RunnerContainer
  26 from .arvjob import ArvadosJob, RunnerJob, RunnerTemplate
  27 from. runner import Runner, upload_instance
  28 from .arvtool import ArvadosCommandTool
  29 from .arvworkflow import ArvadosWorkflow, upload_workflow
  30 from .fsaccess import CollectionFsAccess
  31 from .perf import Perf
  32 from .pathmapper import FinalOutputPathMapper
  33 from ._version import __version__
  34
  35 from cwltool.pack import pack
  36 from cwltool.process import shortname, UnsupportedRequirement, getListing
  37 from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
  38 from cwltool.draft2tool import compute_checksums
  39 from arvados.api import OrderedJsonModel
  40
  41 logger = logging.getLogger('arvados.cwl-runner')
  42 metrics = logging.getLogger('arvados.cwl-runner.metrics')
  43 logger.setLevel(logging.INFO)
  44
  45
  46 class ArvCwlRunner(object):
  47     """Execute a CWL tool or workflow, submit work (using either jobs or
  48     containers API), wait for them to complete, and report output.
  49
  50     """
  51
  52     def __init__(self, api_client, work_api=None, keep_client=None, output_name=None, output_tags=None):
  53         self.api = api_client
  54         self.processes = {}
  55         self.lock = threading.Lock()
  56         self.cond = threading.Condition(self.lock)
  57         self.final_output = None
  58         self.final_status = None
  59         self.uploaded = {}
  60         self.num_retries = 4
  61         self.uuid = None
  62         self.stop_polling = threading.Event()
  63         self.poll_api = None
  64         self.pipeline = None
  65         self.final_output_collection = None
  66         self.output_name = output_name
  67         self.output_tags = output_tags
  68         self.project_uuid = None
  69
  70         if keep_client is not None:
  71             self.keep_client = keep_client
  72         else:
  73             self.keep_client = arvados.keep.KeepClient(api_client=self.api, num_retries=self.num_retries)
  74
  75         for api in ["jobs", "containers"]:
  76             try:
  77                 methods = self.api._rootDesc.get('resources')[api]['methods']
  78                 if ('httpMethod' in methods['create'] and
  79                     (work_api == api or work_api is None)):
  80                     self.work_api = api
  81                     break
  82             except KeyError:
  83                 pass
  84         if not self.work_api:
  85             if work_api is None:
  86                 raise Exception("No supported APIs")
  87             else:
  88                 raise Exception("Unsupported API '%s'" % work_api)
  89
  90     def arv_make_tool(self, toolpath_object, **kwargs):
  91         kwargs["work_api"] = self.work_api
  92         if "class" in toolpath_object and toolpath_object["class"] == "CommandLineTool":
  93             return ArvadosCommandTool(self, toolpath_object, **kwargs)
  94         elif "class" in toolpath_object and toolpath_object["class"] == "Workflow":
  95             return ArvadosWorkflow(self, toolpath_object, **kwargs)
  96         else:
  97             return cwltool.workflow.defaultMakeTool(toolpath_object, **kwargs)
  98
  99     def output_callback(self, out, processStatus):
 100         if processStatus == "success":
 101             logger.info("Overall process status is %s", processStatus)
 102             if self.pipeline:
 103                 self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
 104                                                      body={"state": "Complete"}).execute(num_retries=self.num_retries)
 105         else:
 106             logger.warn("Overall process status is %s", processStatus)
 107             if self.pipeline:
 108                 self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
 109                                                      body={"state": "Failed"}).execute(num_retries=self.num_retries)
 110         self.final_status = processStatus
 111         self.final_output = out
 112
 113     def on_message(self, event):
 114         if "object_uuid" in event:
 115             if event["object_uuid"] in self.processes and event["event_type"] == "update":
 116                 if event["properties"]["new_attributes"]["state"] == "Running" and self.processes[event["object_uuid"]].running is False:
 117                     uuid = event["object_uuid"]
 118                     with self.lock:
 119                         j = self.processes[uuid]
 120                         logger.info("Job %s (%s) is Running", j.name, uuid)
 121                         j.running = True
 122                         j.update_pipeline_component(event["properties"]["new_attributes"])
 123                 elif event["properties"]["new_attributes"]["state"] in ("Complete", "Failed", "Cancelled"):
 124                     uuid = event["object_uuid"]
 125                     try:
 126                         self.cond.acquire()
 127                         j = self.processes[uuid]
 128                         txt = self.work_api[0].upper() + self.work_api[1:-1]
 129                         logger.info("%s %s (%s) is %s", txt, j.name, uuid, event["properties"]["new_attributes"]["state"])
 130                         with Perf(metrics, "done %s" % j.name):
 131                             j.done(event["properties"]["new_attributes"])
 132                         self.cond.notify()
 133                     finally:
 134                         self.cond.release()
 135
 136     def poll_states(self):
 137         """Poll status of jobs or containers listed in the processes dict.
 138
 139         Runs in a separate thread.
 140         """
 141
 142         try:
 143             while True:
 144                 self.stop_polling.wait(15)
 145                 if self.stop_polling.is_set():
 146                     break
 147                 with self.lock:
 148                     keys = self.processes.keys()
 149                 if not keys:
 150                     continue
 151
 152                 if self.work_api == "containers":
 153                     table = self.poll_api.containers()
 154                 elif self.work_api == "jobs":
 155                     table = self.poll_api.jobs()
 156
 157                 try:
 158                     proc_states = table.list(filters=[["uuid", "in", keys]]).execute(num_retries=self.num_retries)
 159                 except Exception as e:
 160                     logger.warn("Error checking states on API server: %s", e)
 161                     continue
 162
 163                 for p in proc_states["items"]:
 164                     self.on_message({
 165                         "object_uuid": p["uuid"],
 166                         "event_type": "update",
 167                         "properties": {
 168                             "new_attributes": p
 169                         }
 170                     })
 171         except:
 172             logger.error("Fatal error in state polling thread.", exc_info=(sys.exc_info()[1] if self.debug else False))
 173             self.cond.acquire()
 174             self.processes.clear()
 175             self.cond.notify()
 176             self.cond.release()
 177         finally:
 178             self.stop_polling.set()
 179
 180     def get_uploaded(self):
 181         return self.uploaded.copy()
 182
 183     def add_uploaded(self, src, pair):
 184         self.uploaded[src] = pair
 185
 186     def check_writable(self, obj):
 187         if isinstance(obj, dict):
 188             if obj.get("writable"):
 189                 raise UnsupportedRequirement("InitialWorkDir feature 'writable: true' not supported")
 190             for v in obj.itervalues():
 191                 self.check_writable(v)
 192         if isinstance(obj, list):
 193             for v in obj:
 194                 self.check_writable(v)
 195
 196     def make_output_collection(self, name, tagsString, outputObj):
 197         outputObj = copy.deepcopy(outputObj)
 198
 199         files = []
 200         def capture(fileobj):
 201             files.append(fileobj)
 202
 203         adjustDirObjs(outputObj, capture)
 204         adjustFileObjs(outputObj, capture)
 205
 206         generatemapper = FinalOutputPathMapper(files, "", "", separateDirs=False)
 207
 208         final = arvados.collection.Collection(api_client=self.api,
 209                                               keep_client=self.keep_client,
 210                                               num_retries=self.num_retries)
 211
 212         srccollections = {}
 213         for k,v in generatemapper.items():
 214             if k.startswith("_:"):
 215                 if v.type == "Directory":
 216                     continue
 217                 if v.type == "CreateFile":
 218                     with final.open(v.target, "wb") as f:
 219                         f.write(v.resolved.encode("utf-8"))
 220                     continue
 221
 222             if not k.startswith("keep:"):
 223                 raise Exception("Output source is not in keep or a literal")
 224             sp = k.split("/")
 225             srccollection = sp[0][5:]
 226             if srccollection not in srccollections:
 227                 try:
 228                     srccollections[srccollection] = arvados.collection.CollectionReader(
 229                         srccollection,
 230                         api_client=self.api,
 231                         keep_client=self.keep_client,
 232                         num_retries=self.num_retries)
 233                 except arvados.errors.ArgumentError as e:
 234                     logger.error("Creating CollectionReader for '%s' '%s': %s", k, v, e)
 235                     raise
 236             reader = srccollections[srccollection]
 237             try:
 238                 srcpath = "/".join(sp[1:]) if len(sp) > 1 else "."
 239                 final.copy(srcpath, v.target, source_collection=reader, overwrite=False)
 240             except IOError as e:
 241                 logger.warn("While preparing output collection: %s", e)
 242
 243         def rewrite(fileobj):
 244             fileobj["location"] = generatemapper.mapper(fileobj["location"]).target
 245             for k in ("basename", "listing", "contents"):
 246                 if k in fileobj:
 247                     del fileobj[k]
 248
 249         adjustDirObjs(outputObj, rewrite)
 250         adjustFileObjs(outputObj, rewrite)
 251
 252         with final.open("cwl.output.json", "w") as f:
 253             json.dump(outputObj, f, sort_keys=True, indent=4, separators=(',',': '))
 254
 255         final.save_new(name=name, owner_uuid=self.project_uuid, ensure_unique_name=True)
 256
 257         logger.info("Final output collection %s \"%s\" (%s)", final.portable_data_hash(),
 258                     final.api_response()["name"],
 259                     final.manifest_locator())
 260
 261         final_uuid = final.manifest_locator()
 262         tags = tagsString.split(',')
 263         for tag in tags:
 264              self.api.links().create(body={
 265                 "head_uuid": final_uuid, "link_class": "tag", "name": tag
 266                 }).execute(num_retries=self.num_retries)
 267
 268         def finalcollection(fileobj):
 269             fileobj["location"] = "keep:%s/%s" % (final.portable_data_hash(), fileobj["location"])
 270
 271         adjustDirObjs(outputObj, finalcollection)
 272         adjustFileObjs(outputObj, finalcollection)
 273
 274         return (outputObj, final)
 275
 276     def set_crunch_output(self):
 277         if self.work_api == "containers":
 278             try:
 279                 current = self.api.containers().current().execute(num_retries=self.num_retries)
 280                 self.api.containers().update(uuid=current['uuid'],
 281                                              body={
 282                                                  'output': self.final_output_collection.portable_data_hash(),
 283                                              }).execute(num_retries=self.num_retries)
 284             except Exception as e:
 285                 logger.info("Setting container output: %s", e)
 286         elif self.work_api == "jobs" and "TASK_UUID" in os.environ:
 287             self.api.job_tasks().update(uuid=os.environ["TASK_UUID"],
 288                                    body={
 289                                        'output': self.final_output_collection.portable_data_hash(),
 290                                        'success': self.final_status == "success",
 291                                        'progress':1.0
 292                                    }).execute(num_retries=self.num_retries)
 293
 294     def arv_executor(self, tool, job_order, **kwargs):
 295         self.debug = kwargs.get("debug")
 296
 297         tool.visit(self.check_writable)
 298
 299         self.project_uuid = kwargs.get("project_uuid")
 300         self.pipeline = None
 301         make_fs_access = kwargs.get("make_fs_access") or partial(CollectionFsAccess,
 302                                                                  api_client=self.api,
 303                                                                  keep_client=self.keep_client)
 304         self.fs_access = make_fs_access(kwargs["basedir"])
 305
 306         existing_uuid = kwargs.get("update_workflow")
 307         if existing_uuid or kwargs.get("create_workflow"):
 308             if self.work_api == "jobs":
 309                 tmpl = RunnerTemplate(self, tool, job_order,
 310                                       kwargs.get("enable_reuse"),
 311                                       uuid=existing_uuid)
 312                 tmpl.save()
 313                 # cwltool.main will write our return value to stdout.
 314                 return tmpl.uuid
 315             else:
 316                 return upload_workflow(self, tool, job_order,
 317                                        self.project_uuid,
 318                                        uuid=existing_uuid)
 319
 320         self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse")
 321
 322         kwargs["make_fs_access"] = make_fs_access
 323         kwargs["enable_reuse"] = kwargs.get("enable_reuse")
 324         kwargs["use_container"] = True
 325         kwargs["tmpdir_prefix"] = "tmp"
 326         kwargs["on_error"] = "continue"
 327         kwargs["compute_checksum"] = kwargs.get("compute_checksum")
 328
 329         if self.work_api == "containers":
 330             kwargs["outdir"] = "/var/spool/cwl"
 331             kwargs["docker_outdir"] = "/var/spool/cwl"
 332             kwargs["tmpdir"] = "/tmp"
 333             kwargs["docker_tmpdir"] = "/tmp"
 334         elif self.work_api == "jobs":
 335             kwargs["outdir"] = "$(task.outdir)"
 336             kwargs["docker_outdir"] = "$(task.outdir)"
 337             kwargs["tmpdir"] = "$(task.tmpdir)"
 338
 339         upload_instance(self, shortname(tool.tool["id"]), tool, job_order)
 340
 341         runnerjob = None
 342         if kwargs.get("submit"):
 343             if self.work_api == "containers":
 344                 if tool.tool["class"] == "CommandLineTool":
 345                     runnerjob = tool.job(job_order,
 346                                          self.output_callback,
 347                                          **kwargs).next()
 348                 else:
 349                     runnerjob = RunnerContainer(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name, self.output_tags)
 350             else:
 351                 runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name, self.output_tags)
 352
 353         if not kwargs.get("submit") and "cwl_runner_job" not in kwargs and not self.work_api == "containers":
 354             # Create pipeline for local run
 355             self.pipeline = self.api.pipeline_instances().create(
 356                 body={
 357                     "owner_uuid": self.project_uuid,
 358                     "name": shortname(tool.tool["id"]),
 359                     "components": {},
 360                     "state": "RunningOnClient"}).execute(num_retries=self.num_retries)
 361             logger.info("Pipeline instance %s", self.pipeline["uuid"])
 362
 363         if runnerjob and not kwargs.get("wait"):
 364             runnerjob.run(wait=kwargs.get("wait"))
 365             return runnerjob.uuid
 366
 367         self.poll_api = arvados.api('v1')
 368         self.polling_thread = threading.Thread(target=self.poll_states)
 369         self.polling_thread.start()
 370
 371         if runnerjob:
 372             jobiter = iter((runnerjob,))
 373         else:
 374             if "cwl_runner_job" in kwargs:
 375                 self.uuid = kwargs.get("cwl_runner_job").get('uuid')
 376             jobiter = tool.job(job_order,
 377                                self.output_callback,
 378                                **kwargs)
 379
 380         try:
 381             self.cond.acquire()
 382             # Will continue to hold the lock for the duration of this code
 383             # except when in cond.wait(), at which point on_message can update
 384             # job state and process output callbacks.
 385
 386             loopperf = Perf(metrics, "jobiter")
 387             loopperf.__enter__()
 388             for runnable in jobiter:
 389                 loopperf.__exit__()
 390
 391                 if self.stop_polling.is_set():
 392                     break
 393
 394                 if runnable:
 395                     with Perf(metrics, "run"):
 396                         runnable.run(**kwargs)
 397                 else:
 398                     if self.processes:
 399                         self.cond.wait(1)
 400                     else:
 401                         logger.error("Workflow is deadlocked, no runnable jobs and not waiting on any pending jobs.")
 402                         break
 403                 loopperf.__enter__()
 404             loopperf.__exit__()
 405
 406             while self.processes:
 407                 self.cond.wait(1)
 408
 409         except UnsupportedRequirement:
 410             raise
 411         except:
 412             if sys.exc_info()[0] is KeyboardInterrupt:
 413                 logger.error("Interrupted, marking pipeline as failed")
 414             else:
 415                 logger.error("Execution failed: %s", sys.exc_info()[1], exc_info=(sys.exc_info()[1] if self.debug else False))
 416             if self.pipeline:
 417                 self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
 418                                                      body={"state": "Failed"}).execute(num_retries=self.num_retries)
 419             if runnerjob and runnerjob.uuid and self.work_api == "containers":
 420                 self.api.container_requests().update(uuid=runnerjob.uuid,
 421                                                      body={"priority": "0"}).execute(num_retries=self.num_retries)
 422         finally:
 423             self.cond.release()
 424             self.stop_polling.set()
 425             self.polling_thread.join()
 426
 427         if self.final_status == "UnsupportedRequirement":
 428             raise UnsupportedRequirement("Check log for details.")
 429
 430         if self.final_output is None:
 431             raise WorkflowException("Workflow did not return a result.")
 432
 433         if kwargs.get("submit") and isinstance(runnerjob, Runner):
 434             logger.info("Final output collection %s", runnerjob.final_output)
 435         else:
 436             if self.output_name is None:
 437                 self.output_name = "Output of %s" % (shortname(tool.tool["id"]))
 438             if self.output_tags is None:
 439                 self.output_tags = ""
 440             self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, self.output_tags, self.final_output)
 441             self.set_crunch_output()
 442
 443         if self.final_status != "success":
 444             raise WorkflowException("Workflow failed.")
 445
 446         if kwargs.get("compute_checksum"):
 447             adjustDirObjs(self.final_output, partial(getListing, self.fs_access))
 448             adjustFileObjs(self.final_output, partial(compute_checksums, self.fs_access))
 449
 450         return self.final_output
 451
 452
 453 def versionstring():
 454     """Print version string of key packages for provenance and debugging."""
 455
 456     arvcwlpkg = pkg_resources.require("arvados-cwl-runner")
 457     arvpkg = pkg_resources.require("arvados-python-client")
 458     cwlpkg = pkg_resources.require("cwltool")
 459
 460     return "%s %s %s, %s %s, %s %s" % (sys.argv[0], __version__, arvcwlpkg[0].version,
 461                                     "arvados-python-client", arvpkg[0].version,
 462                                     "cwltool", cwlpkg[0].version)
 463
 464
 465 def arg_parser():  # type: () -> argparse.ArgumentParser
 466     parser = argparse.ArgumentParser(description='Arvados executor for Common Workflow Language')
 467
 468     parser.add_argument("--basedir", type=str,
 469                         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).")
 470     parser.add_argument("--outdir", type=str, default=os.path.abspath('.'),
 471                         help="Output directory, default current directory")
 472
 473     parser.add_argument("--eval-timeout",
 474                         help="Time to wait for a Javascript expression to evaluate before giving an error, default 20s.",
 475                         type=float,
 476                         default=20)
 477     parser.add_argument("--version", action="store_true", help="Print version and exit")
 478
 479     exgroup = parser.add_mutually_exclusive_group()
 480     exgroup.add_argument("--verbose", action="store_true", help="Default logging")
 481     exgroup.add_argument("--quiet", action="store_true", help="Only print warnings and errors.")
 482     exgroup.add_argument("--debug", action="store_true", help="Print even more logging")
 483
 484     parser.add_argument("--metrics", action="store_true", help="Print timing metrics")
 485
 486     parser.add_argument("--tool-help", action="store_true", help="Print command line help for tool")
 487
 488     exgroup = parser.add_mutually_exclusive_group()
 489     exgroup.add_argument("--enable-reuse", action="store_true",
 490                         default=True, dest="enable_reuse",
 491                         help="")
 492     exgroup.add_argument("--disable-reuse", action="store_false",
 493                         default=True, dest="enable_reuse",
 494                         help="")
 495
 496     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.")
 497     parser.add_argument("--output-name", type=str, help="Name to use for collection that stores the final output.", default=None)
 498     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)
 499     parser.add_argument("--ignore-docker-for-reuse", action="store_true",
 500                         help="Ignore Docker image version when deciding whether to reuse past jobs.",
 501                         default=False)
 502
 503     exgroup = parser.add_mutually_exclusive_group()
 504     exgroup.add_argument("--submit", action="store_true", help="Submit workflow to run on Arvados.",
 505                         default=True, dest="submit")
 506     exgroup.add_argument("--local", action="store_false", help="Run workflow on local host (submits jobs to Arvados).",
 507                         default=True, dest="submit")
 508     exgroup.add_argument("--create-template", action="store_true", help="(Deprecated) synonym for --create-workflow.",
 509                          dest="create_workflow")
 510     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.")
 511     exgroup.add_argument("--update-workflow", type=str, metavar="UUID", help="Update an existing Arvados workflow or pipeline template with the given UUID.")
 512
 513     exgroup = parser.add_mutually_exclusive_group()
 514     exgroup.add_argument("--wait", action="store_true", help="After submitting workflow runner job, wait for completion.",
 515                         default=True, dest="wait")
 516     exgroup.add_argument("--no-wait", action="store_false", help="Submit workflow runner job and exit.",
 517                         default=True, dest="wait")
 518
 519     parser.add_argument("--api", type=str,
 520                         default=None, dest="work_api",
 521                         help="Select work submission API, one of 'jobs' or 'containers'. Default is 'jobs' if that API is available, otherwise 'containers'.")
 522
 523     parser.add_argument("--compute-checksum", action="store_true", default=False,
 524                         help="Compute checksum of contents while collecting outputs",
 525                         dest="compute_checksum")
 526
 527     parser.add_argument("workflow", type=str, nargs="?", default=None, help="The workflow to execute")
 528     parser.add_argument("job_order", nargs=argparse.REMAINDER, help="The input object to the workflow.")
 529
 530     return parser
 531
 532 def add_arv_hints():
 533     cache = {}
 534     res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml')
 535     cache["http://arvados.org/cwl"] = res.read()
 536     res.close()
 537     document_loader, cwlnames, _, _ = cwltool.process.get_schema("v1.0")
 538     _, extnames, _, _ = schema_salad.schema.load_schema("http://arvados.org/cwl", cache=cache)
 539     for n in extnames.names:
 540         if not cwlnames.has_name("http://arvados.org/cwl#"+n, ""):
 541             cwlnames.add_name("http://arvados.org/cwl#"+n, "", extnames.get_name(n, ""))
 542         document_loader.idx["http://arvados.org/cwl#"+n] = {}
 543
 544 def main(args, stdout, stderr, api_client=None, keep_client=None):
 545     parser = arg_parser()
 546
 547     job_order_object = None
 548     arvargs = parser.parse_args(args)
 549
 550     if arvargs.update_workflow:
 551         if arvargs.update_workflow.find('-7fd4e-') == 5:
 552             want_api = 'containers'
 553         elif arvargs.update_workflow.find('-p5p6p-') == 5:
 554             want_api = 'jobs'
 555         else:
 556             want_api = None
 557         if want_api and arvargs.work_api and want_api != arvargs.work_api:
 558             logger.error('--update-workflow arg {!r} uses {!r} API, but --api={!r} specified'.format(
 559                 arvargs.update_workflow, want_api, arvargs.work_api))
 560             return 1
 561         arvargs.work_api = want_api
 562
 563     if (arvargs.create_workflow or arvargs.update_workflow) and not arvargs.job_order:
 564         job_order_object = ({}, "")
 565
 566     add_arv_hints()
 567
 568     try:
 569         if api_client is None:
 570             api_client=arvados.api('v1', model=OrderedJsonModel())
 571         runner = ArvCwlRunner(api_client, work_api=arvargs.work_api, keep_client=keep_client, output_name=arvargs.output_name, output_tags=arvargs.output_tags)
 572     except Exception as e:
 573         logger.error(e)
 574         return 1
 575
 576     if arvargs.debug:
 577         logger.setLevel(logging.DEBUG)
 578
 579     if arvargs.quiet:
 580         logger.setLevel(logging.WARN)
 581         logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
 582
 583     if arvargs.metrics:
 584         metrics.setLevel(logging.DEBUG)
 585         logging.getLogger("cwltool.metrics").setLevel(logging.DEBUG)
 586
 587     arvargs.conformance_test = None
 588     arvargs.use_container = True
 589
 590     return cwltool.main.main(args=arvargs,
 591                              stdout=stdout,
 592                              stderr=stderr,
 593                              executor=runner.arv_executor,
 594                              makeTool=runner.arv_make_tool,
 595                              versionfunc=versionstring,
 596                              job_order_object=job_order_object,
 597                              make_fs_access=partial(CollectionFsAccess, api_client=api_client))