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 cwltool.process
  21 import schema_salad
  22 from schema_salad.sourceline import SourceLine
  23
  24 import arvados
  25 import arvados.config
  26 from arvados.keep import KeepClient
  27 from arvados.errors import ApiError
  28
  29 from .arvcontainer import ArvadosContainer, RunnerContainer
  30 from .arvjob import ArvadosJob, RunnerJob, RunnerTemplate
  31 from. runner import Runner, upload_instance
  32 from .arvtool import ArvadosCommandTool
  33 from .arvworkflow import ArvadosWorkflow, upload_workflow
  34 from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver
  35 from .perf import Perf
  36 from .pathmapper import FinalOutputPathMapper
  37 from ._version import __version__
  38
  39 from cwltool.pack import pack
  40 from cwltool.process import shortname, UnsupportedRequirement, getListing
  41 from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
  42 from cwltool.draft2tool import compute_checksums
  43 from arvados.api import OrderedJsonModel
  44
  45 logger = logging.getLogger('arvados.cwl-runner')
  46 metrics = logging.getLogger('arvados.cwl-runner.metrics')
  47 logger.setLevel(logging.INFO)
  48
  49 arvados.log_handler.setFormatter(logging.Formatter(
  50         '%(asctime)s %(name)s %(levelname)s: %(message)s',
  51         '%Y-%m-%d %H:%M:%S'))
  52
  53 class ArvCwlRunner(object):
  54     """Execute a CWL tool or workflow, submit work (using either jobs or
  55     containers API), wait for them to complete, and report output.
  56
  57     """
  58
  59     def __init__(self, api_client, work_api=None, keep_client=None, output_name=None, output_tags=None, num_retries=4):
  60         self.api = api_client
  61         self.processes = {}
  62         self.lock = threading.Lock()
  63         self.cond = threading.Condition(self.lock)
  64         self.final_output = None
  65         self.final_status = None
  66         self.uploaded = {}
  67         self.num_retries = num_retries
  68         self.uuid = None
  69         self.stop_polling = threading.Event()
  70         self.poll_api = None
  71         self.pipeline = None
  72         self.final_output_collection = None
  73         self.output_name = output_name
  74         self.output_tags = output_tags
  75         self.project_uuid = None
  76
  77         if keep_client is not None:
  78             self.keep_client = keep_client
  79         else:
  80             self.keep_client = arvados.keep.KeepClient(api_client=self.api, num_retries=self.num_retries)
  81
  82         self.work_api = None
  83         expected_api = ["jobs", "containers"]
  84         for api in expected_api:
  85             try:
  86                 methods = self.api._rootDesc.get('resources')[api]['methods']
  87                 if ('httpMethod' in methods['create'] and
  88                     (work_api == api or work_api is None)):
  89                     self.work_api = api
  90                     break
  91             except KeyError:
  92                 pass
  93
  94         if not self.work_api:
  95             if work_api is None:
  96                 raise Exception("No supported APIs")
  97             else:
  98                 raise Exception("Unsupported API '%s', expected one of %s" % (work_api, expected_api))
  99
 100     def arv_make_tool(self, toolpath_object, **kwargs):
 101         kwargs["work_api"] = self.work_api
 102         kwargs["fetcher_constructor"] = partial(CollectionFetcher,
 103                                                 api_client=self.api,
 104                                                 keep_client=self.keep_client)
 105         if "class" in toolpath_object and toolpath_object["class"] == "CommandLineTool":
 106             return ArvadosCommandTool(self, toolpath_object, **kwargs)
 107         elif "class" in toolpath_object and toolpath_object["class"] == "Workflow":
 108             return ArvadosWorkflow(self, toolpath_object, **kwargs)
 109         else:
 110             return cwltool.workflow.defaultMakeTool(toolpath_object, **kwargs)
 111
 112     def output_callback(self, out, processStatus):
 113         if processStatus == "success":
 114             logger.info("Overall process status is %s", processStatus)
 115             if self.pipeline:
 116                 self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
 117                                                      body={"state": "Complete"}).execute(num_retries=self.num_retries)
 118         else:
 119             logger.warn("Overall process status is %s", processStatus)
 120             if self.pipeline:
 121                 self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
 122                                                      body={"state": "Failed"}).execute(num_retries=self.num_retries)
 123         self.final_status = processStatus
 124         self.final_output = out
 125
 126     def on_message(self, event):
 127         if "object_uuid" in event:
 128             if event["object_uuid"] in self.processes and event["event_type"] == "update":
 129                 if event["properties"]["new_attributes"]["state"] == "Running" and self.processes[event["object_uuid"]].running is False:
 130                     uuid = event["object_uuid"]
 131                     with self.lock:
 132                         j = self.processes[uuid]
 133                         logger.info("%s %s is Running", self.label(j), uuid)
 134                         j.running = True
 135                         j.update_pipeline_component(event["properties"]["new_attributes"])
 136                 elif event["properties"]["new_attributes"]["state"] in ("Complete", "Failed", "Cancelled", "Final"):
 137                     uuid = event["object_uuid"]
 138                     try:
 139                         self.cond.acquire()
 140                         j = self.processes[uuid]
 141                         logger.info("%s %s is %s", self.label(j), uuid, event["properties"]["new_attributes"]["state"])
 142                         with Perf(metrics, "done %s" % j.name):
 143                             j.done(event["properties"]["new_attributes"])
 144                         self.cond.notify()
 145                     finally:
 146                         self.cond.release()
 147
 148     def label(self, obj):
 149         return "[%s %s]" % (self.work_api[0:-1], obj.name)
 150
 151     def poll_states(self):
 152         """Poll status of jobs or containers listed in the processes dict.
 153
 154         Runs in a separate thread.
 155         """
 156
 157         try:
 158             while True:
 159                 self.stop_polling.wait(15)
 160                 if self.stop_polling.is_set():
 161                     break
 162                 with self.lock:
 163                     keys = self.processes.keys()
 164                 if not keys:
 165                     continue
 166
 167                 if self.work_api == "containers":
 168                     table = self.poll_api.container_requests()
 169                 elif self.work_api == "jobs":
 170                     table = self.poll_api.jobs()
 171
 172                 try:
 173                     proc_states = table.list(filters=[["uuid", "in", keys]]).execute(num_retries=self.num_retries)
 174                 except Exception as e:
 175                     logger.warn("Error checking states on API server: %s", e)
 176                     continue
 177
 178                 for p in proc_states["items"]:
 179                     self.on_message({
 180                         "object_uuid": p["uuid"],
 181                         "event_type": "update",
 182                         "properties": {
 183                             "new_attributes": p
 184                         }
 185                     })
 186         except:
 187             logger.error("Fatal error in state polling thread.", exc_info=(sys.exc_info()[1] if self.debug else False))
 188             self.cond.acquire()
 189             self.processes.clear()
 190             self.cond.notify()
 191             self.cond.release()
 192         finally:
 193             self.stop_polling.set()
 194
 195     def get_uploaded(self):
 196         return self.uploaded.copy()
 197
 198     def add_uploaded(self, src, pair):
 199         self.uploaded[src] = pair
 200
 201     def check_features(self, obj):
 202         if isinstance(obj, dict):
 203             if obj.get("class") == "InitialWorkDirRequirement":
 204                 if self.work_api == "containers":
 205                     raise UnsupportedRequirement("InitialWorkDirRequirement not supported with --api=containers")
 206             if obj.get("writable"):
 207                 raise SourceLine(obj, "writable", UnsupportedRequirement).makeError("InitialWorkDir feature 'writable: true' not supported")
 208             if obj.get("class") == "CommandLineTool":
 209                 if self.work_api == "containers":
 210                     if obj.get("stdin"):
 211                         raise SourceLine(obj, "stdin", UnsupportedRequirement).makeError("Stdin redirection currently not suppported with --api=containers")
 212                     if obj.get("stderr"):
 213                         raise SourceLine(obj, "stderr", UnsupportedRequirement).makeError("Stderr redirection currently not suppported with --api=containers")
 214             for v in obj.itervalues():
 215                 self.check_features(v)
 216         elif isinstance(obj, list):
 217             for i,v in enumerate(obj):
 218                 with SourceLine(obj, i, UnsupportedRequirement):
 219                     self.check_features(v)
 220
 221     def make_output_collection(self, name, tagsString, outputObj):
 222         outputObj = copy.deepcopy(outputObj)
 223
 224         files = []
 225         def capture(fileobj):
 226             files.append(fileobj)
 227
 228         adjustDirObjs(outputObj, capture)
 229         adjustFileObjs(outputObj, capture)
 230
 231         generatemapper = FinalOutputPathMapper(files, "", "", separateDirs=False)
 232
 233         final = arvados.collection.Collection(api_client=self.api,
 234                                               keep_client=self.keep_client,
 235                                               num_retries=self.num_retries)
 236
 237         srccollections = {}
 238         for k,v in generatemapper.items():
 239             if k.startswith("_:"):
 240                 if v.type == "Directory":
 241                     continue
 242                 if v.type == "CreateFile":
 243                     with final.open(v.target, "wb") as f:
 244                         f.write(v.resolved.encode("utf-8"))
 245                     continue
 246
 247             if not k.startswith("keep:"):
 248                 raise Exception("Output source is not in keep or a literal")
 249             sp = k.split("/")
 250             srccollection = sp[0][5:]
 251             if srccollection not in srccollections:
 252                 try:
 253                     srccollections[srccollection] = arvados.collection.CollectionReader(
 254                         srccollection,
 255                         api_client=self.api,
 256                         keep_client=self.keep_client,
 257                         num_retries=self.num_retries)
 258                 except arvados.errors.ArgumentError as e:
 259                     logger.error("Creating CollectionReader for '%s' '%s': %s", k, v, e)
 260                     raise
 261             reader = srccollections[srccollection]
 262             try:
 263                 srcpath = "/".join(sp[1:]) if len(sp) > 1 else "."
 264                 final.copy(srcpath, v.target, source_collection=reader, overwrite=False)
 265             except IOError as e:
 266                 logger.warn("While preparing output collection: %s", e)
 267
 268         def rewrite(fileobj):
 269             fileobj["location"] = generatemapper.mapper(fileobj["location"]).target
 270             for k in ("basename", "listing", "contents"):
 271                 if k in fileobj:
 272                     del fileobj[k]
 273
 274         adjustDirObjs(outputObj, rewrite)
 275         adjustFileObjs(outputObj, rewrite)
 276
 277         with final.open("cwl.output.json", "w") as f:
 278             json.dump(outputObj, f, sort_keys=True, indent=4, separators=(',',': '))
 279
 280         final.save_new(name=name, owner_uuid=self.project_uuid, ensure_unique_name=True)
 281
 282         logger.info("Final output collection %s \"%s\" (%s)", final.portable_data_hash(),
 283                     final.api_response()["name"],
 284                     final.manifest_locator())
 285
 286         final_uuid = final.manifest_locator()
 287         tags = tagsString.split(',')
 288         for tag in tags:
 289              self.api.links().create(body={
 290                 "head_uuid": final_uuid, "link_class": "tag", "name": tag
 291                 }).execute(num_retries=self.num_retries)
 292
 293         def finalcollection(fileobj):
 294             fileobj["location"] = "keep:%s/%s" % (final.portable_data_hash(), fileobj["location"])
 295
 296         adjustDirObjs(outputObj, finalcollection)
 297         adjustFileObjs(outputObj, finalcollection)
 298
 299         return (outputObj, final)
 300
 301     def set_crunch_output(self):
 302         if self.work_api == "containers":
 303             try:
 304                 current = self.api.containers().current().execute(num_retries=self.num_retries)
 305             except ApiError as e:
 306                 # Status code 404 just means we're not running in a container.
 307                 if e.resp.status != 404:
 308                     logger.info("Getting current container: %s", e)
 309                 return
 310             try:
 311                 self.api.containers().update(uuid=current['uuid'],
 312                                              body={
 313                                                  'output': self.final_output_collection.portable_data_hash(),
 314                                              }).execute(num_retries=self.num_retries)
 315             except Exception as e:
 316                 logger.info("Setting container output: %s", e)
 317         elif self.work_api == "jobs" and "TASK_UUID" in os.environ:
 318             self.api.job_tasks().update(uuid=os.environ["TASK_UUID"],
 319                                    body={
 320                                        'output': self.final_output_collection.portable_data_hash(),
 321                                        'success': self.final_status == "success",
 322                                        'progress':1.0
 323                                    }).execute(num_retries=self.num_retries)
 324
 325     def arv_executor(self, tool, job_order, **kwargs):
 326         self.debug = kwargs.get("debug")
 327
 328         tool.visit(self.check_features)
 329
 330         self.project_uuid = kwargs.get("project_uuid")
 331         self.pipeline = None
 332         make_fs_access = kwargs.get("make_fs_access") or partial(CollectionFsAccess,
 333                                                                  api_client=self.api,
 334                                                                  keep_client=self.keep_client)
 335         self.fs_access = make_fs_access(kwargs["basedir"])
 336
 337         existing_uuid = kwargs.get("update_workflow")
 338         if existing_uuid or kwargs.get("create_workflow"):
 339             if self.work_api == "jobs":
 340                 tmpl = RunnerTemplate(self, tool, job_order,
 341                                       kwargs.get("enable_reuse"),
 342                                       uuid=existing_uuid,
 343                                       submit_runner_ram=kwargs.get("submit_runner_ram"),
 344                                       name=kwargs.get("name"))
 345                 tmpl.save()
 346                 # cwltool.main will write our return value to stdout.
 347                 return tmpl.uuid
 348             else:
 349                 return upload_workflow(self, tool, job_order,
 350                                        self.project_uuid,
 351                                        uuid=existing_uuid,
 352                                        submit_runner_ram=kwargs.get("submit_runner_ram"),
 353                                        name=kwargs.get("name"))
 354
 355         self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse")
 356
 357         kwargs["make_fs_access"] = make_fs_access
 358         kwargs["enable_reuse"] = kwargs.get("enable_reuse")
 359         kwargs["use_container"] = True
 360         kwargs["tmpdir_prefix"] = "tmp"
 361         kwargs["on_error"] = "continue"
 362         kwargs["compute_checksum"] = kwargs.get("compute_checksum")
 363
 364         if not kwargs["name"]:
 365             del kwargs["name"]
 366
 367         if self.work_api == "containers":
 368             kwargs["outdir"] = "/var/spool/cwl"
 369             kwargs["docker_outdir"] = "/var/spool/cwl"
 370             kwargs["tmpdir"] = "/tmp"
 371             kwargs["docker_tmpdir"] = "/tmp"
 372         elif self.work_api == "jobs":
 373             kwargs["outdir"] = "$(task.outdir)"
 374             kwargs["docker_outdir"] = "$(task.outdir)"
 375             kwargs["tmpdir"] = "$(task.tmpdir)"
 376
 377         upload_instance(self, shortname(tool.tool["id"]), tool, job_order)
 378
 379         runnerjob = None
 380         if kwargs.get("submit"):
 381             if self.work_api == "containers":
 382                 if tool.tool["class"] == "CommandLineTool":
 383                     kwargs["runnerjob"] = tool.tool["id"]
 384                     runnerjob = tool.job(job_order,
 385                                          self.output_callback,
 386                                          **kwargs).next()
 387                 else:
 388                     runnerjob = RunnerContainer(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name,
 389                                                 self.output_tags, submit_runner_ram=kwargs.get("submit_runner_ram"),
 390                                                 name=kwargs.get("name"))
 391             else:
 392                 runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name,
 393                                       self.output_tags, submit_runner_ram=kwargs.get("submit_runner_ram"),
 394                                       name=kwargs.get("name"))
 395
 396         if not kwargs.get("submit") and "cwl_runner_job" not in kwargs and not self.work_api == "containers":
 397             # Create pipeline for local run
 398             self.pipeline = self.api.pipeline_instances().create(
 399                 body={
 400                     "owner_uuid": self.project_uuid,
 401                     "name": kwargs["name"] if kwargs.get("name") else shortname(tool.tool["id"]),
 402                     "components": {},
 403                     "state": "RunningOnClient"}).execute(num_retries=self.num_retries)
 404             logger.info("Pipeline instance %s", self.pipeline["uuid"])
 405
 406         if runnerjob and not kwargs.get("wait"):
 407             runnerjob.run(wait=kwargs.get("wait"))
 408             return runnerjob.uuid
 409
 410         self.poll_api = arvados.api('v1')
 411         self.polling_thread = threading.Thread(target=self.poll_states)
 412         self.polling_thread.start()
 413
 414         if runnerjob:
 415             jobiter = iter((runnerjob,))
 416         else:
 417             if "cwl_runner_job" in kwargs:
 418                 self.uuid = kwargs.get("cwl_runner_job").get('uuid')
 419             jobiter = tool.job(job_order,
 420                                self.output_callback,
 421                                **kwargs)
 422
 423         try:
 424             self.cond.acquire()
 425             # Will continue to hold the lock for the duration of this code
 426             # except when in cond.wait(), at which point on_message can update
 427             # job state and process output callbacks.
 428
 429             loopperf = Perf(metrics, "jobiter")
 430             loopperf.__enter__()
 431             for runnable in jobiter:
 432                 loopperf.__exit__()
 433
 434                 if self.stop_polling.is_set():
 435                     break
 436
 437                 if runnable:
 438                     with Perf(metrics, "run"):
 439                         runnable.run(**kwargs)
 440                 else:
 441                     if self.processes:
 442                         self.cond.wait(1)
 443                     else:
 444                         logger.error("Workflow is deadlocked, no runnable jobs and not waiting on any pending jobs.")
 445                         break
 446                 loopperf.__enter__()
 447             loopperf.__exit__()
 448
 449             while self.processes:
 450                 self.cond.wait(1)
 451
 452         except UnsupportedRequirement:
 453             raise
 454         except:
 455             if sys.exc_info()[0] is KeyboardInterrupt:
 456                 logger.error("Interrupted, marking pipeline as failed")
 457             else:
 458                 logger.error("Execution failed: %s", sys.exc_info()[1], exc_info=(sys.exc_info()[1] if self.debug else False))
 459             if self.pipeline:
 460                 self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
 461                                                      body={"state": "Failed"}).execute(num_retries=self.num_retries)
 462             if runnerjob and runnerjob.uuid and self.work_api == "containers":
 463                 self.api.container_requests().update(uuid=runnerjob.uuid,
 464                                                      body={"priority": "0"}).execute(num_retries=self.num_retries)
 465         finally:
 466             self.cond.release()
 467             self.stop_polling.set()
 468             self.polling_thread.join()
 469
 470         if self.final_status == "UnsupportedRequirement":
 471             raise UnsupportedRequirement("Check log for details.")
 472
 473         if self.final_output is None:
 474             raise WorkflowException("Workflow did not return a result.")
 475
 476         if kwargs.get("submit") and isinstance(runnerjob, Runner):
 477             logger.info("Final output collection %s", runnerjob.final_output)
 478         else:
 479             if self.output_name is None:
 480                 self.output_name = "Output of %s" % (shortname(tool.tool["id"]))
 481             if self.output_tags is None:
 482                 self.output_tags = ""
 483             self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, self.output_tags, self.final_output)
 484             self.set_crunch_output()
 485
 486         if self.final_status != "success":
 487             raise WorkflowException("Workflow failed.")
 488
 489         if kwargs.get("compute_checksum"):
 490             adjustDirObjs(self.final_output, partial(getListing, self.fs_access))
 491             adjustFileObjs(self.final_output, partial(compute_checksums, self.fs_access))
 492
 493         return self.final_output
 494
 495
 496 def versionstring():
 497     """Print version string of key packages for provenance and debugging."""
 498
 499     arvcwlpkg = pkg_resources.require("arvados-cwl-runner")
 500     arvpkg = pkg_resources.require("arvados-python-client")
 501     cwlpkg = pkg_resources.require("cwltool")
 502
 503     return "%s %s %s, %s %s, %s %s" % (sys.argv[0], __version__, arvcwlpkg[0].version,
 504                                     "arvados-python-client", arvpkg[0].version,
 505                                     "cwltool", cwlpkg[0].version)
 506
 507
 508 def arg_parser():  # type: () -> argparse.ArgumentParser
 509     parser = argparse.ArgumentParser(description='Arvados executor for Common Workflow Language')
 510
 511     parser.add_argument("--basedir", type=str,
 512                         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).")
 513     parser.add_argument("--outdir", type=str, default=os.path.abspath('.'),
 514                         help="Output directory, default current directory")
 515
 516     parser.add_argument("--eval-timeout",
 517                         help="Time to wait for a Javascript expression to evaluate before giving an error, default 20s.",
 518                         type=float,
 519                         default=20)
 520     parser.add_argument("--version", action="store_true", help="Print version and exit")
 521
 522     exgroup = parser.add_mutually_exclusive_group()
 523     exgroup.add_argument("--verbose", action="store_true", help="Default logging")
 524     exgroup.add_argument("--quiet", action="store_true", help="Only print warnings and errors.")
 525     exgroup.add_argument("--debug", action="store_true", help="Print even more logging")
 526
 527     parser.add_argument("--metrics", action="store_true", help="Print timing metrics")
 528
 529     parser.add_argument("--tool-help", action="store_true", help="Print command line help for tool")
 530
 531     exgroup = parser.add_mutually_exclusive_group()
 532     exgroup.add_argument("--enable-reuse", action="store_true",
 533                         default=True, dest="enable_reuse",
 534                         help="")
 535     exgroup.add_argument("--disable-reuse", action="store_false",
 536                         default=True, dest="enable_reuse",
 537                         help="")
 538
 539     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.")
 540     parser.add_argument("--output-name", type=str, help="Name to use for collection that stores the final output.", default=None)
 541     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)
 542     parser.add_argument("--ignore-docker-for-reuse", action="store_true",
 543                         help="Ignore Docker image version when deciding whether to reuse past jobs.",
 544                         default=False)
 545
 546     exgroup = parser.add_mutually_exclusive_group()
 547     exgroup.add_argument("--submit", action="store_true", help="Submit workflow to run on Arvados.",
 548                         default=True, dest="submit")
 549     exgroup.add_argument("--local", action="store_false", help="Run workflow on local host (submits jobs to Arvados).",
 550                         default=True, dest="submit")
 551     exgroup.add_argument("--create-template", action="store_true", help="(Deprecated) synonym for --create-workflow.",
 552                          dest="create_workflow")
 553     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.")
 554     exgroup.add_argument("--update-workflow", type=str, metavar="UUID", help="Update an existing Arvados workflow or pipeline template with the given UUID.")
 555
 556     exgroup = parser.add_mutually_exclusive_group()
 557     exgroup.add_argument("--wait", action="store_true", help="After submitting workflow runner job, wait for completion.",
 558                         default=True, dest="wait")
 559     exgroup.add_argument("--no-wait", action="store_false", help="Submit workflow runner job and exit.",
 560                         default=True, dest="wait")
 561
 562     exgroup = parser.add_mutually_exclusive_group()
 563     exgroup.add_argument("--log-timestamps", action="store_true", help="Prefix logging lines with timestamp",
 564                         default=True, dest="log_timestamps")
 565     exgroup.add_argument("--no-log-timestamps", action="store_false", help="No timestamp on logging lines",
 566                         default=True, dest="log_timestamps")
 567
 568     parser.add_argument("--api", type=str,
 569                         default=None, dest="work_api",
 570                         help="Select work submission API, one of 'jobs' or 'containers'. Default is 'jobs' if that API is available, otherwise 'containers'.")
 571
 572     parser.add_argument("--compute-checksum", action="store_true", default=False,
 573                         help="Compute checksum of contents while collecting outputs",
 574                         dest="compute_checksum")
 575
 576     parser.add_argument("--submit-runner-ram", type=int,
 577                         help="RAM (in MiB) required for the workflow runner job (default 1024)",
 578                         default=1024)
 579
 580     parser.add_argument("--name", type=str,
 581                         help="Name to use for workflow execution instance.",
 582                         default=None)
 583
 584     parser.add_argument("workflow", type=str, nargs="?", default=None, help="The workflow to execute")
 585     parser.add_argument("job_order", nargs=argparse.REMAINDER, help="The input object to the workflow.")
 586
 587     return parser
 588
 589 def add_arv_hints():
 590     cache = {}
 591     res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml')
 592     cache["http://arvados.org/cwl"] = res.read()
 593     res.close()
 594     document_loader, cwlnames, _, _ = cwltool.process.get_schema("v1.0")
 595     _, extnames, _, _ = schema_salad.schema.load_schema("http://arvados.org/cwl", cache=cache)
 596     for n in extnames.names:
 597         if not cwlnames.has_name("http://arvados.org/cwl#"+n, ""):
 598             cwlnames.add_name("http://arvados.org/cwl#"+n, "", extnames.get_name(n, ""))
 599         document_loader.idx["http://arvados.org/cwl#"+n] = {}
 600
 601 def main(args, stdout, stderr, api_client=None, keep_client=None):
 602     parser = arg_parser()
 603
 604     job_order_object = None
 605     arvargs = parser.parse_args(args)
 606
 607     if arvargs.version:
 608         print versionstring()
 609         return
 610
 611     if arvargs.update_workflow:
 612         if arvargs.update_workflow.find('-7fd4e-') == 5:
 613             want_api = 'containers'
 614         elif arvargs.update_workflow.find('-p5p6p-') == 5:
 615             want_api = 'jobs'
 616         else:
 617             want_api = None
 618         if want_api and arvargs.work_api and want_api != arvargs.work_api:
 619             logger.error('--update-workflow arg {!r} uses {!r} API, but --api={!r} specified'.format(
 620                 arvargs.update_workflow, want_api, arvargs.work_api))
 621             return 1
 622         arvargs.work_api = want_api
 623
 624     if (arvargs.create_workflow or arvargs.update_workflow) and not arvargs.job_order:
 625         job_order_object = ({}, "")
 626
 627     add_arv_hints()
 628
 629     try:
 630         if api_client is None:
 631             api_client=arvados.api('v1', model=OrderedJsonModel())
 632         if keep_client is None:
 633             keep_client = arvados.keep.KeepClient(api_client=api_client, num_retries=4)
 634         runner = ArvCwlRunner(api_client, work_api=arvargs.work_api, keep_client=keep_client,
 635                               num_retries=4, output_name=arvargs.output_name,
 636                               output_tags=arvargs.output_tags)
 637     except Exception as e:
 638         logger.error(e)
 639         return 1
 640
 641     if arvargs.debug:
 642         logger.setLevel(logging.DEBUG)
 643
 644     if arvargs.quiet:
 645         logger.setLevel(logging.WARN)
 646         logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
 647
 648     if arvargs.metrics:
 649         metrics.setLevel(logging.DEBUG)
 650         logging.getLogger("cwltool.metrics").setLevel(logging.DEBUG)
 651
 652     if arvargs.log_timestamps:
 653         arvados.log_handler.setFormatter(logging.Formatter(
 654             '%(asctime)s %(name)s %(levelname)s: %(message)s',
 655             '%Y-%m-%d %H:%M:%S'))
 656     else:
 657         arvados.log_handler.setFormatter(logging.Formatter('%(name)s %(levelname)s: %(message)s'))
 658
 659     arvargs.conformance_test = None
 660     arvargs.use_container = True
 661     arvargs.relax_path_checks = True
 662     arvargs.validate = None
 663
 664     return cwltool.main.main(args=arvargs,
 665                              stdout=stdout,
 666                              stderr=stderr,
 667                              executor=runner.arv_executor,
 668                              makeTool=runner.arv_make_tool,
 669                              versionfunc=versionstring,
 670                              job_order_object=job_order_object,
 671                              make_fs_access=partial(CollectionFsAccess,
 672                                                     api_client=api_client,
 673                                                     keep_client=keep_client),
 674                              fetcher_constructor=partial(CollectionFetcher,
 675                                                          api_client=api_client,
 676                                                          keep_client=keep_client),
 677                              resolver=partial(collectionResolver, api_client),
 678                              logger_handler=arvados.log_handler)