sdk/cwl/arvados_cwl/executor.py

   1 # Copyright (C) The Arvados Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: Apache-2.0
   4
   5 from __future__ import division
   6 from builtins import next
   7 from builtins import object
   8 from builtins import str
   9 from future.utils import viewvalues, viewitems
  10
  11 import argparse
  12 import logging
  13 import os
  14 import sys
  15 import threading
  16 import copy
  17 import json
  18 import re
  19 from functools import partial
  20 import subprocess
  21 import time
  22 import urllib
  23
  24 from cwltool.errors import WorkflowException
  25 import cwltool.workflow
  26 from schema_salad.sourceline import SourceLine
  27 import schema_salad.validate as validate
  28 from schema_salad.ref_resolver import file_uri, uri_file_path
  29
  30 import arvados
  31 import arvados.config
  32 from arvados.keep import KeepClient
  33 from arvados.errors import ApiError
  34
  35 import arvados_cwl.util
  36 from .arvcontainer import RunnerContainer, cleanup_name_for_collection
  37 from .runner import Runner, upload_docker, upload_job_order, upload_workflow_deps, make_builder
  38 from .arvtool import ArvadosCommandTool, validate_cluster_target, ArvadosExpressionTool
  39 from .arvworkflow import ArvadosWorkflow, upload_workflow
  40 from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver, CollectionCache, pdh_size
  41 from .perf import Perf
  42 from .pathmapper import NoFollowPathMapper
  43 from cwltool.task_queue import TaskQueue
  44 from .context import ArvLoadingContext, ArvRuntimeContext
  45 from ._version import __version__
  46
  47 from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema
  48 from cwltool.utils import adjustFileObjs, adjustDirObjs, get_listing, visit_class, aslist
  49 from cwltool.command_line_tool import compute_checksums
  50 from cwltool.load_tool import load_tool
  51
  52 logger = logging.getLogger('arvados.cwl-runner')
  53 metrics = logging.getLogger('arvados.cwl-runner.metrics')
  54
  55 DEFAULT_PRIORITY = 500
  56
  57 class RuntimeStatusLoggingHandler(logging.Handler):
  58     """
  59     Intercepts logging calls and report them as runtime statuses on runner
  60     containers.
  61     """
  62     def __init__(self, runtime_status_update_func):
  63         super(RuntimeStatusLoggingHandler, self).__init__()
  64         self.runtime_status_update = runtime_status_update_func
  65         self.updatingRuntimeStatus = False
  66
  67     def emit(self, record):
  68         kind = None
  69         if record.levelno >= logging.ERROR:
  70             kind = 'error'
  71         elif record.levelno >= logging.WARNING:
  72             kind = 'warning'
  73         if kind == 'warning' and record.name == "salad":
  74             # Don't send validation warnings to runtime status,
  75             # they're noisy and unhelpful.
  76             return
  77         if kind is not None and self.updatingRuntimeStatus is not True:
  78             self.updatingRuntimeStatus = True
  79             try:
  80                 log_msg = record.getMessage()
  81                 if '\n' in log_msg:
  82                     # If the logged message is multi-line, use its first line as status
  83                     # and the rest as detail.
  84                     status, detail = log_msg.split('\n', 1)
  85                     self.runtime_status_update(
  86                         kind,
  87                         "%s: %s" % (record.name, status),
  88                         detail
  89                     )
  90                 else:
  91                     self.runtime_status_update(
  92                         kind,
  93                         "%s: %s" % (record.name, record.getMessage())
  94                     )
  95             finally:
  96                 self.updatingRuntimeStatus = False
  97
  98
  99 class ArvCwlExecutor(object):
 100     """Execute a CWL tool or workflow, submit work (using containers API),
 101     wait for them to complete, and report output.
 102
 103     """
 104
 105     def __init__(self, api_client,
 106                  arvargs=None,
 107                  keep_client=None,
 108                  num_retries=4,
 109                  thread_count=4,
 110                  stdout=sys.stdout):
 111
 112         if arvargs is None:
 113             arvargs = argparse.Namespace()
 114             arvargs.work_api = None
 115             arvargs.output_name = None
 116             arvargs.output_tags = None
 117             arvargs.thread_count = 1
 118             arvargs.collection_cache_size = None
 119             arvargs.git_info = True
 120             arvargs.submit = False
 121             arvargs.defer_downloads = False
 122
 123         self.api = api_client
 124         self.processes = {}
 125         self.workflow_eval_lock = threading.Condition(threading.RLock())
 126         self.final_output = None
 127         self.final_status = None
 128         self.num_retries = num_retries
 129         self.uuid = None
 130         self.stop_polling = threading.Event()
 131         self.poll_api = None
 132         self.pipeline = None
 133         self.final_output_collection = None
 134         self.output_name = arvargs.output_name
 135         self.output_tags = arvargs.output_tags
 136         self.project_uuid = None
 137         self.intermediate_output_ttl = 0
 138         self.intermediate_output_collections = []
 139         self.trash_intermediate = False
 140         self.thread_count = arvargs.thread_count
 141         self.poll_interval = 12
 142         self.loadingContext = None
 143         self.should_estimate_cache_size = True
 144         self.fs_access = None
 145         self.secret_store = None
 146         self.stdout = stdout
 147         self.fast_submit = False
 148         self.git_info = arvargs.git_info
 149
 150         if keep_client is not None:
 151             self.keep_client = keep_client
 152         else:
 153             self.keep_client = arvados.keep.KeepClient(api_client=self.api, num_retries=self.num_retries)
 154
 155         if arvargs.collection_cache_size:
 156             collection_cache_size = arvargs.collection_cache_size*1024*1024
 157             self.should_estimate_cache_size = False
 158         else:
 159             collection_cache_size = 256*1024*1024
 160
 161         self.collection_cache = CollectionCache(self.api, self.keep_client, self.num_retries,
 162                                                 cap=collection_cache_size)
 163
 164         self.fetcher_constructor = partial(CollectionFetcher,
 165                                            api_client=self.api,
 166                                            fs_access=CollectionFsAccess("", collection_cache=self.collection_cache),
 167                                            num_retries=self.num_retries)
 168
 169         self.work_api = None
 170         expected_api = ["containers"]
 171         for api in expected_api:
 172             try:
 173                 methods = self.api._rootDesc.get('resources')[api]['methods']
 174                 if ('httpMethod' in methods['create'] and
 175                     (arvargs.work_api == api or arvargs.work_api is None)):
 176                     self.work_api = api
 177                     break
 178             except KeyError:
 179                 pass
 180
 181         if not self.work_api:
 182             if arvargs.work_api is None:
 183                 raise Exception("No supported APIs")
 184             else:
 185                 raise Exception("Unsupported API '%s', expected one of %s" % (arvargs.work_api, expected_api))
 186
 187         if self.work_api == "jobs":
 188             logger.error("""
 189 *******************************
 190 The 'jobs' API is no longer supported.
 191 *******************************""")
 192             exit(1)
 193
 194         self.loadingContext = ArvLoadingContext(vars(arvargs))
 195         self.loadingContext.fetcher_constructor = self.fetcher_constructor
 196         self.loadingContext.resolver = partial(collectionResolver, self.api, num_retries=self.num_retries)
 197         self.loadingContext.construct_tool_object = self.arv_make_tool
 198
 199         # Add a custom logging handler to the root logger for runtime status reporting
 200         # if running inside a container
 201         if arvados_cwl.util.get_current_container(self.api, self.num_retries, logger):
 202             root_logger = logging.getLogger('')
 203
 204             # Remove existing RuntimeStatusLoggingHandlers if they exist
 205             handlers = [h for h in root_logger.handlers if not isinstance(h, RuntimeStatusLoggingHandler)]
 206             root_logger.handlers = handlers
 207
 208             handler = RuntimeStatusLoggingHandler(self.runtime_status_update)
 209             root_logger.addHandler(handler)
 210
 211         self.toplevel_runtimeContext = ArvRuntimeContext(vars(arvargs))
 212         self.toplevel_runtimeContext.make_fs_access = partial(CollectionFsAccess,
 213                                                      collection_cache=self.collection_cache)
 214
 215         self.defer_downloads = arvargs.submit and arvargs.defer_downloads
 216
 217         validate_cluster_target(self, self.toplevel_runtimeContext)
 218
 219
 220     def arv_make_tool(self, toolpath_object, loadingContext):
 221         if "class" in toolpath_object and toolpath_object["class"] == "CommandLineTool":
 222             return ArvadosCommandTool(self, toolpath_object, loadingContext)
 223         elif "class" in toolpath_object and toolpath_object["class"] == "Workflow":
 224             return ArvadosWorkflow(self, toolpath_object, loadingContext)
 225         elif "class" in toolpath_object and toolpath_object["class"] == "ExpressionTool":
 226             return ArvadosExpressionTool(self, toolpath_object, loadingContext)
 227         else:
 228             raise Exception("Unknown tool %s" % toolpath_object.get("class"))
 229
 230     def output_callback(self, out, processStatus):
 231         with self.workflow_eval_lock:
 232             if processStatus == "success":
 233                 logger.info("Overall process status is %s", processStatus)
 234                 state = "Complete"
 235             else:
 236                 logger.error("Overall process status is %s", processStatus)
 237                 state = "Failed"
 238             if self.pipeline:
 239                 self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
 240                                                         body={"state": state}).execute(num_retries=self.num_retries)
 241             self.final_status = processStatus
 242             self.final_output = out
 243             self.workflow_eval_lock.notifyAll()
 244
 245
 246     def start_run(self, runnable, runtimeContext):
 247         self.task_queue.add(partial(runnable.run, runtimeContext),
 248                             self.workflow_eval_lock, self.stop_polling)
 249
 250     def process_submitted(self, container):
 251         with self.workflow_eval_lock:
 252             self.processes[container.uuid] = container
 253
 254     def process_done(self, uuid, record):
 255         with self.workflow_eval_lock:
 256             j = self.processes[uuid]
 257             logger.info("%s %s is %s", self.label(j), uuid, record["state"])
 258             self.task_queue.add(partial(j.done, record),
 259                                 self.workflow_eval_lock, self.stop_polling)
 260             del self.processes[uuid]
 261
 262     def runtime_status_update(self, kind, message, detail=None):
 263         """
 264         Updates the runtime_status field on the runner container.
 265         Called when there's a need to report errors, warnings or just
 266         activity statuses, for example in the RuntimeStatusLoggingHandler.
 267         """
 268
 269         if kind not in ('error', 'warning'):
 270             # Ignore any other status kind
 271             return
 272
 273         with self.workflow_eval_lock:
 274             current = None
 275             try:
 276                 current = arvados_cwl.util.get_current_container(self.api, self.num_retries, logger)
 277             except Exception as e:
 278                 logger.info("Couldn't get current container: %s", e)
 279             if current is None:
 280                 return
 281             runtime_status = current.get('runtime_status', {})
 282
 283             original_updatemessage = updatemessage = runtime_status.get(kind, "")
 284             if not updatemessage:
 285                 updatemessage = message
 286
 287             # Subsequent messages tacked on in detail
 288             original_updatedetail = updatedetail = runtime_status.get(kind+'Detail', "")
 289             maxlines = 40
 290             if updatedetail.count("\n") < maxlines:
 291                 if updatedetail:
 292                     updatedetail += "\n"
 293                 updatedetail += message + "\n"
 294
 295                 if detail:
 296                     updatedetail += detail + "\n"
 297
 298                 if updatedetail.count("\n") >= maxlines:
 299                     updatedetail += "\nSome messages may have been omitted.  Check the full log."
 300
 301             if updatemessage == original_updatemessage and updatedetail == original_updatedetail:
 302                 # don't waste time doing an update if nothing changed
 303                 # (usually because we exceeded the max lines)
 304                 return
 305
 306             runtime_status.update({
 307                 kind: updatemessage,
 308                 kind+'Detail': updatedetail,
 309             })
 310
 311             try:
 312                 self.api.containers().update(uuid=current['uuid'],
 313                                             body={
 314                                                 'runtime_status': runtime_status,
 315                                             }).execute(num_retries=self.num_retries)
 316             except Exception as e:
 317                 logger.info("Couldn't update runtime_status: %s", e)
 318
 319     def wrapped_callback(self, cb, obj, st):
 320         with self.workflow_eval_lock:
 321             cb(obj, st)
 322             self.workflow_eval_lock.notifyAll()
 323
 324     def get_wrapped_callback(self, cb):
 325         return partial(self.wrapped_callback, cb)
 326
 327     def on_message(self, event):
 328         if event.get("object_uuid") in self.processes and event["event_type"] == "update":
 329             uuid = event["object_uuid"]
 330             if event["properties"]["new_attributes"]["state"] == "Running":
 331                 with self.workflow_eval_lock:
 332                     j = self.processes[uuid]
 333                     if j.running is False:
 334                         j.running = True
 335                         j.update_pipeline_component(event["properties"]["new_attributes"])
 336                         logger.info("%s %s is Running", self.label(j), uuid)
 337             elif event["properties"]["new_attributes"]["state"] in ("Complete", "Failed", "Cancelled", "Final"):
 338                 self.process_done(uuid, event["properties"]["new_attributes"])
 339
 340     def label(self, obj):
 341         return "[%s %s]" % (self.work_api[0:-1], obj.name)
 342
 343     def poll_states(self):
 344         """Poll status of containers listed in the processes dict.
 345
 346         Runs in a separate thread.
 347         """
 348
 349         try:
 350             remain_wait = self.poll_interval
 351             while True:
 352                 if remain_wait > 0:
 353                     self.stop_polling.wait(remain_wait)
 354                 if self.stop_polling.is_set():
 355                     break
 356                 with self.workflow_eval_lock:
 357                     keys = list(self.processes)
 358                 if not keys:
 359                     remain_wait = self.poll_interval
 360                     continue
 361
 362                 begin_poll = time.time()
 363                 if self.work_api == "containers":
 364                     table = self.poll_api.container_requests()
 365
 366                 pageSize = self.poll_api._rootDesc.get('maxItemsPerResponse', 1000)
 367
 368                 while keys:
 369                     page = keys[:pageSize]
 370                     try:
 371                         proc_states = table.list(filters=[["uuid", "in", page]]).execute(num_retries=self.num_retries)
 372                     except Exception as e:
 373                         logger.exception("Error checking states on API server: %s", e)
 374                         remain_wait = self.poll_interval
 375                         continue
 376
 377                     for p in proc_states["items"]:
 378                         self.on_message({
 379                             "object_uuid": p["uuid"],
 380                             "event_type": "update",
 381                             "properties": {
 382                                 "new_attributes": p
 383                             }
 384                         })
 385                     keys = keys[pageSize:]
 386
 387                 finish_poll = time.time()
 388                 remain_wait = self.poll_interval - (finish_poll - begin_poll)
 389         except:
 390             logger.exception("Fatal error in state polling thread.")
 391             with self.workflow_eval_lock:
 392                 self.processes.clear()
 393                 self.workflow_eval_lock.notifyAll()
 394         finally:
 395             self.stop_polling.set()
 396
 397     def add_intermediate_output(self, uuid):
 398         if uuid:
 399             self.intermediate_output_collections.append(uuid)
 400
 401     def trash_intermediate_output(self):
 402         logger.info("Cleaning up intermediate output collections")
 403         for i in self.intermediate_output_collections:
 404             try:
 405                 self.api.collections().delete(uuid=i).execute(num_retries=self.num_retries)
 406             except Exception:
 407                 logger.warning("Failed to delete intermediate output: %s", sys.exc_info()[1], exc_info=(sys.exc_info()[1] if self.debug else False))
 408             except (KeyboardInterrupt, SystemExit):
 409                 break
 410
 411     def check_features(self, obj, parentfield=""):
 412         if isinstance(obj, dict):
 413             if obj.get("class") == "DockerRequirement":
 414                 if obj.get("dockerOutputDirectory"):
 415                     if not obj.get("dockerOutputDirectory").startswith('/'):
 416                         raise SourceLine(obj, "dockerOutputDirectory", validate.ValidationException).makeError(
 417                             "Option 'dockerOutputDirectory' must be an absolute path.")
 418             if obj.get("class") == "InplaceUpdateRequirement":
 419                 if obj["inplaceUpdate"] and parentfield == "requirements":
 420                     raise SourceLine(obj, "class", UnsupportedRequirement).makeError("InplaceUpdateRequirement not supported for keep collections.")
 421             for k,v in viewitems(obj):
 422                 self.check_features(v, parentfield=k)
 423         elif isinstance(obj, list):
 424             for i,v in enumerate(obj):
 425                 with SourceLine(obj, i, UnsupportedRequirement, logger.isEnabledFor(logging.DEBUG)):
 426                     self.check_features(v, parentfield=parentfield)
 427
 428     def make_output_collection(self, name, storage_classes, tagsString, output_properties, outputObj):
 429         outputObj = copy.deepcopy(outputObj)
 430
 431         files = []
 432         def capture(fileobj):
 433             files.append(fileobj)
 434
 435         adjustDirObjs(outputObj, capture)
 436         adjustFileObjs(outputObj, capture)
 437
 438         generatemapper = NoFollowPathMapper(files, "", "", separateDirs=False)
 439
 440         final = arvados.collection.Collection(api_client=self.api,
 441                                               keep_client=self.keep_client,
 442                                               num_retries=self.num_retries)
 443
 444         for k,v in generatemapper.items():
 445             if v.type == "Directory" and v.resolved.startswith("_:"):
 446                     continue
 447             if v.type == "CreateFile" and (k.startswith("_:") or v.resolved.startswith("_:")):
 448                 with final.open(v.target, "wb") as f:
 449                     f.write(v.resolved.encode("utf-8"))
 450                     continue
 451
 452             if not v.resolved.startswith("keep:"):
 453                 raise Exception("Output source is not in keep or a literal")
 454             sp = v.resolved.split("/")
 455             srccollection = sp[0][5:]
 456             try:
 457                 reader = self.collection_cache.get(srccollection)
 458                 srcpath = urllib.parse.unquote("/".join(sp[1:]) if len(sp) > 1 else ".")
 459                 final.copy(srcpath, v.target, source_collection=reader, overwrite=False)
 460             except arvados.errors.ArgumentError as e:
 461                 logger.error("Creating CollectionReader for '%s' '%s': %s", k, v, e)
 462                 raise
 463             except IOError as e:
 464                 logger.error("While preparing output collection: %s", e)
 465                 raise
 466
 467         def rewrite(fileobj):
 468             fileobj["location"] = generatemapper.mapper(fileobj["location"]).target
 469             for k in ("listing", "contents", "nameext", "nameroot", "dirname"):
 470                 if k in fileobj:
 471                     del fileobj[k]
 472
 473         adjustDirObjs(outputObj, rewrite)
 474         adjustFileObjs(outputObj, rewrite)
 475
 476         with final.open("cwl.output.json", "w") as f:
 477             res = str(json.dumps(outputObj, sort_keys=True, indent=4, separators=(',',': '), ensure_ascii=False))
 478             f.write(res)
 479
 480
 481         final.save_new(name=name, owner_uuid=self.project_uuid, storage_classes=storage_classes,
 482                        ensure_unique_name=True, properties=output_properties)
 483
 484         logger.info("Final output collection %s \"%s\" (%s)", final.portable_data_hash(),
 485                     final.api_response()["name"],
 486                     final.manifest_locator())
 487
 488         final_uuid = final.manifest_locator()
 489         tags = tagsString.split(',')
 490         for tag in tags:
 491              self.api.links().create(body={
 492                 "head_uuid": final_uuid, "link_class": "tag", "name": tag
 493                 }).execute(num_retries=self.num_retries)
 494
 495         def finalcollection(fileobj):
 496             fileobj["location"] = "keep:%s/%s" % (final.portable_data_hash(), fileobj["location"])
 497
 498         adjustDirObjs(outputObj, finalcollection)
 499         adjustFileObjs(outputObj, finalcollection)
 500
 501         return (outputObj, final)
 502
 503     def set_crunch_output(self):
 504         if self.work_api == "containers":
 505             current = arvados_cwl.util.get_current_container(self.api, self.num_retries, logger)
 506             if current is None:
 507                 return
 508             try:
 509                 self.api.containers().update(uuid=current['uuid'],
 510                                              body={
 511                                                  'output': self.final_output_collection.portable_data_hash(),
 512                                                  'output_properties': self.final_output_collection.get_properties(),
 513                                              }).execute(num_retries=self.num_retries)
 514                 self.api.collections().update(uuid=self.final_output_collection.manifest_locator(),
 515                                               body={
 516                                                   'is_trashed': True
 517                                               }).execute(num_retries=self.num_retries)
 518             except Exception:
 519                 logger.exception("Setting container output")
 520                 raise
 521
 522     def apply_reqs(self, job_order_object, tool):
 523         if "https://w3id.org/cwl/cwl#requirements" in job_order_object:
 524             if tool.metadata.get("http://commonwl.org/cwltool#original_cwlVersion") == 'v1.0':
 525                 raise WorkflowException(
 526                     "`cwl:requirements` in the input object is not part of CWL "
 527                     "v1.0. You can adjust to use `cwltool:overrides` instead; or you "
 528                     "can set the cwlVersion to v1.1 or greater and re-run with "
 529                     "--enable-dev.")
 530             job_reqs = job_order_object["https://w3id.org/cwl/cwl#requirements"]
 531             for req in job_reqs:
 532                 tool.requirements.append(req)
 533
 534     @staticmethod
 535     def get_git_info(tool):
 536         in_a_git_repo = False
 537         cwd = None
 538         filepath = None
 539
 540         if tool.tool["id"].startswith("file://"):
 541             # check if git is installed
 542             try:
 543                 filepath = uri_file_path(tool.tool["id"])
 544                 cwd = os.path.dirname(filepath)
 545                 subprocess.run(["git", "log", "--format=%H", "-n1", "HEAD"], cwd=cwd, check=True, capture_output=True, text=True)
 546                 in_a_git_repo = True
 547             except Exception as e:
 548                 pass
 549
 550         gitproperties = {}
 551
 552         if in_a_git_repo:
 553             git_commit = subprocess.run(["git", "log", "--format=%H", "-n1", "HEAD"], cwd=cwd, capture_output=True, text=True).stdout
 554             git_date = subprocess.run(["git", "log", "--format=%cD", "-n1", "HEAD"], cwd=cwd, capture_output=True, text=True).stdout
 555             git_committer = subprocess.run(["git", "log", "--format=%cn <%ce>", "-n1", "HEAD"], cwd=cwd, capture_output=True, text=True).stdout
 556             git_branch = subprocess.run(["git", "rev-parse", "--abbrev-ref", "HEAD"], cwd=cwd, capture_output=True, text=True).stdout
 557             git_origin = subprocess.run(["git", "remote", "get-url", "origin"], cwd=cwd, capture_output=True, text=True).stdout
 558             git_status = subprocess.run(["git", "status", "--untracked-files=no", "--porcelain"], cwd=cwd, capture_output=True, text=True).stdout
 559             git_describe = subprocess.run(["git", "describe", "--always", "--tags"], cwd=cwd, capture_output=True, text=True).stdout
 560             git_toplevel = subprocess.run(["git", "rev-parse", "--show-toplevel"], cwd=cwd, capture_output=True, text=True).stdout
 561             git_path = filepath[len(git_toplevel):]
 562
 563             gitproperties = {
 564                 "http://arvados.org/cwl#gitCommit": git_commit.strip(),
 565                 "http://arvados.org/cwl#gitDate": git_date.strip(),
 566                 "http://arvados.org/cwl#gitCommitter": git_committer.strip(),
 567                 "http://arvados.org/cwl#gitBranch": git_branch.strip(),
 568                 "http://arvados.org/cwl#gitOrigin": git_origin.strip(),
 569                 "http://arvados.org/cwl#gitStatus": git_status.strip(),
 570                 "http://arvados.org/cwl#gitDescribe": git_describe.strip(),
 571                 "http://arvados.org/cwl#gitPath": git_path.strip(),
 572             }
 573         else:
 574             for g in ("http://arvados.org/cwl#gitCommit",
 575                       "http://arvados.org/cwl#gitDate",
 576                       "http://arvados.org/cwl#gitCommitter",
 577                       "http://arvados.org/cwl#gitBranch",
 578                       "http://arvados.org/cwl#gitOrigin",
 579                       "http://arvados.org/cwl#gitStatus",
 580                       "http://arvados.org/cwl#gitDescribe",
 581                       "http://arvados.org/cwl#gitPath"):
 582                 if g in tool.metadata:
 583                     gitproperties[g] = tool.metadata[g]
 584
 585         return gitproperties
 586
 587     def set_container_request_properties(self, container, properties):
 588         resp = self.api.container_requests().list(filters=[["container_uuid", "=", container["uuid"]]], select=["uuid", "properties"]).execute(num_retries=self.num_retries)
 589         for cr in resp["items"]:
 590             cr["properties"].update({k.replace("http://arvados.org/cwl#", "arv:"): v for k, v in properties.items()})
 591             self.api.container_requests().update(uuid=cr["uuid"], body={"container_request": {"properties": cr["properties"]}}).execute(num_retries=self.num_retries)
 592
 593     def arv_executor(self, updated_tool, job_order, runtimeContext, logger=None):
 594         self.debug = runtimeContext.debug
 595
 596         git_info = self.get_git_info(updated_tool) if self.git_info else {}
 597         if git_info:
 598             logger.info("Git provenance")
 599             for g in git_info:
 600                 if git_info[g]:
 601                     logger.info("  %s: %s", g.split("#", 1)[1], git_info[g])
 602
 603         workbench1 = self.api.config()["Services"]["Workbench1"]["ExternalURL"]
 604         workbench2 = self.api.config()["Services"]["Workbench2"]["ExternalURL"]
 605         controller = self.api.config()["Services"]["Controller"]["ExternalURL"]
 606         logger.info("Using cluster %s (%s)", self.api.config()["ClusterID"], workbench2 or workbench1 or controller)
 607
 608         if not self.fast_submit:
 609             updated_tool.visit(self.check_features)
 610
 611         self.pipeline = None
 612         self.fs_access = runtimeContext.make_fs_access(runtimeContext.basedir)
 613         self.secret_store = runtimeContext.secret_store
 614
 615         self.trash_intermediate = runtimeContext.trash_intermediate
 616         if self.trash_intermediate and self.work_api != "containers":
 617             raise Exception("--trash-intermediate is only supported with --api=containers.")
 618
 619         self.intermediate_output_ttl = runtimeContext.intermediate_output_ttl
 620         if self.intermediate_output_ttl and self.work_api != "containers":
 621             raise Exception("--intermediate-output-ttl is only supported with --api=containers.")
 622         if self.intermediate_output_ttl < 0:
 623             raise Exception("Invalid value %d for --intermediate-output-ttl, cannot be less than zero" % self.intermediate_output_ttl)
 624
 625         if runtimeContext.submit_request_uuid and self.work_api != "containers":
 626             raise Exception("--submit-request-uuid requires containers API, but using '{}' api".format(self.work_api))
 627
 628         runtimeContext = runtimeContext.copy()
 629
 630         default_storage_classes = ",".join([k for k,v in self.api.config().get("StorageClasses", {"default": {"Default": True}}).items() if v.get("Default") is True])
 631         if runtimeContext.storage_classes == "default":
 632             runtimeContext.storage_classes = default_storage_classes
 633         if runtimeContext.intermediate_storage_classes == "default":
 634             runtimeContext.intermediate_storage_classes = default_storage_classes
 635
 636         if not runtimeContext.name:
 637             self.name = updated_tool.tool.get("label") or updated_tool.metadata.get("label") or os.path.basename(updated_tool.tool["id"])
 638             if git_info.get("http://arvados.org/cwl#gitDescribe"):
 639                 self.name = "%s (%s)" % (self.name, git_info.get("http://arvados.org/cwl#gitDescribe"))
 640             runtimeContext.name = self.name
 641
 642         if runtimeContext.copy_deps is None and (runtimeContext.create_workflow or runtimeContext.update_workflow):
 643             # When creating or updating workflow record, by default
 644             # always copy dependencies and ensure Docker images are up
 645             # to date.
 646             runtimeContext.copy_deps = True
 647             runtimeContext.match_local_docker = True
 648
 649         if runtimeContext.update_workflow and self.project_uuid is None:
 650             # If we are updating a workflow, make sure anything that
 651             # gets uploaded goes into the same parent project, unless
 652             # an alternate --project-uuid was provided.
 653             existing_wf = self.api.workflows().get(uuid=runtimeContext.update_workflow).execute()
 654             runtimeContext.project_uuid = existing_wf["owner_uuid"]
 655
 656         self.project_uuid = runtimeContext.project_uuid
 657
 658         # Upload local file references in the job order.
 659         with Perf(metrics, "upload_job_order"):
 660             job_order = upload_job_order(self, "%s input" % runtimeContext.name,
 661                                          updated_tool, job_order, runtimeContext)
 662
 663         # the last clause means: if it is a command line tool, and we
 664         # are going to wait for the result, and always_submit_runner
 665         # is false, then we don't submit a runner process.
 666
 667         submitting = (runtimeContext.update_workflow or
 668                       runtimeContext.create_workflow or
 669                       (runtimeContext.submit and not
 670                        (updated_tool.tool["class"] == "CommandLineTool" and
 671                         runtimeContext.wait and
 672                         not runtimeContext.always_submit_runner)))
 673
 674         loadingContext = self.loadingContext.copy()
 675         loadingContext.do_validate = False
 676         loadingContext.disable_js_validation = True
 677         if submitting and not self.fast_submit:
 678             loadingContext.do_update = False
 679             # Document may have been auto-updated. Reload the original
 680             # document with updating disabled because we want to
 681             # submit the document with its original CWL version, not
 682             # the auto-updated one.
 683             with Perf(metrics, "load_tool original"):
 684                 tool = load_tool(updated_tool.tool["id"], loadingContext)
 685         else:
 686             tool = updated_tool
 687
 688         # Upload direct dependencies of workflow steps, get back mapping of files to keep references.
 689         # Also uploads docker images.
 690         if not self.fast_submit:
 691             logger.info("Uploading workflow dependencies")
 692             with Perf(metrics, "upload_workflow_deps"):
 693                 merged_map = upload_workflow_deps(self, tool, runtimeContext)
 694         else:
 695             merged_map = {}
 696
 697         # Recreate process object (ArvadosWorkflow or
 698         # ArvadosCommandTool) because tool document may have been
 699         # updated by upload_workflow_deps in ways that modify
 700         # inheritance of hints or requirements.
 701         loadingContext.loader = tool.doc_loader
 702         loadingContext.avsc_names = tool.doc_schema
 703         loadingContext.metadata = tool.metadata
 704         with Perf(metrics, "load_tool"):
 705             tool = load_tool(tool.tool, loadingContext)
 706
 707         if runtimeContext.update_workflow or runtimeContext.create_workflow:
 708             # Create a pipeline template or workflow record and exit.
 709             if self.work_api == "containers":
 710                 uuid = upload_workflow(self, tool, job_order,
 711                                        runtimeContext.project_uuid,
 712                                        runtimeContext,
 713                                        uuid=runtimeContext.update_workflow,
 714                                        submit_runner_ram=runtimeContext.submit_runner_ram,
 715                                        name=runtimeContext.name,
 716                                        merged_map=merged_map,
 717                                        submit_runner_image=runtimeContext.submit_runner_image,
 718                                        git_info=git_info)
 719                 self.stdout.write(uuid + "\n")
 720                 return (None, "success")
 721
 722         self.apply_reqs(job_order, tool)
 723
 724         self.ignore_docker_for_reuse = runtimeContext.ignore_docker_for_reuse
 725         self.eval_timeout = runtimeContext.eval_timeout
 726
 727         runtimeContext.use_container = True
 728         runtimeContext.tmpdir_prefix = "tmp"
 729         runtimeContext.work_api = self.work_api
 730
 731         if not self.output_name:
 732              self.output_name = "Output from workflow %s" % runtimeContext.name
 733
 734         self.output_name  = cleanup_name_for_collection(self.output_name)
 735
 736         if self.work_api == "containers":
 737             if self.ignore_docker_for_reuse:
 738                 raise Exception("--ignore-docker-for-reuse not supported with containers API.")
 739             runtimeContext.outdir = "/var/spool/cwl"
 740             runtimeContext.docker_outdir = "/var/spool/cwl"
 741             runtimeContext.tmpdir = "/tmp"
 742             runtimeContext.docker_tmpdir = "/tmp"
 743
 744         if runtimeContext.priority < 1 or runtimeContext.priority > 1000:
 745             raise Exception("--priority must be in the range 1..1000.")
 746
 747         if self.should_estimate_cache_size:
 748             visited = set()
 749             estimated_size = [0]
 750             def estimate_collection_cache(obj):
 751                 if obj.get("location", "").startswith("keep:"):
 752                     m = pdh_size.match(obj["location"][5:])
 753                     if m and m.group(1) not in visited:
 754                         visited.add(m.group(1))
 755                         estimated_size[0] += int(m.group(2))
 756             visit_class(job_order, ("File", "Directory"), estimate_collection_cache)
 757             runtimeContext.collection_cache_size = max(((estimated_size[0]*192) // (1024*1024))+1, 256)
 758             self.collection_cache.set_cap(runtimeContext.collection_cache_size*1024*1024)
 759
 760         logger.info("Using collection cache size %s MiB", runtimeContext.collection_cache_size)
 761
 762         runnerjob = None
 763         if runtimeContext.submit:
 764             # Submit a runner job to run the workflow for us.
 765             if self.work_api == "containers":
 766                 if submitting:
 767                     tool = RunnerContainer(self, updated_tool,
 768                                            tool, loadingContext, runtimeContext.enable_reuse,
 769                                            self.output_name,
 770                                            self.output_tags,
 771                                            submit_runner_ram=runtimeContext.submit_runner_ram,
 772                                            name=runtimeContext.name,
 773                                            on_error=runtimeContext.on_error,
 774                                            submit_runner_image=runtimeContext.submit_runner_image,
 775                                            intermediate_output_ttl=runtimeContext.intermediate_output_ttl,
 776                                            merged_map=merged_map,
 777                                            priority=runtimeContext.priority,
 778                                            secret_store=self.secret_store,
 779                                            collection_cache_size=runtimeContext.collection_cache_size,
 780                                            collection_cache_is_default=self.should_estimate_cache_size,
 781                                            git_info=git_info)
 782                 else:
 783                     runtimeContext.runnerjob = tool.tool["id"]
 784
 785         if runtimeContext.cwl_runner_job is not None:
 786             self.uuid = runtimeContext.cwl_runner_job.get('uuid')
 787
 788         jobiter = tool.job(job_order,
 789                            self.output_callback,
 790                            runtimeContext)
 791
 792         if runtimeContext.submit and not runtimeContext.wait:
 793             runnerjob = next(jobiter)
 794             runnerjob.run(runtimeContext)
 795             self.stdout.write(runnerjob.uuid+"\n")
 796             return (None, "success")
 797
 798         current_container = arvados_cwl.util.get_current_container(self.api, self.num_retries, logger)
 799         if current_container:
 800             logger.info("Running inside container %s", current_container.get("uuid"))
 801             self.set_container_request_properties(current_container, git_info)
 802
 803         self.poll_api = arvados.api('v1', timeout=runtimeContext.http_timeout)
 804         self.polling_thread = threading.Thread(target=self.poll_states)
 805         self.polling_thread.start()
 806
 807         self.task_queue = TaskQueue(self.workflow_eval_lock, self.thread_count)
 808
 809         try:
 810             self.workflow_eval_lock.acquire()
 811
 812             # Holds the lock while this code runs and releases it when
 813             # it is safe to do so in self.workflow_eval_lock.wait(),
 814             # at which point on_message can update job state and
 815             # process output callbacks.
 816
 817             loopperf = Perf(metrics, "jobiter")
 818             loopperf.__enter__()
 819             for runnable in jobiter:
 820                 loopperf.__exit__()
 821
 822                 if self.stop_polling.is_set():
 823                     break
 824
 825                 if self.task_queue.error is not None:
 826                     raise self.task_queue.error
 827
 828                 if runnable:
 829                     with Perf(metrics, "run"):
 830                         self.start_run(runnable, runtimeContext)
 831                 else:
 832                     if (self.task_queue.in_flight + len(self.processes)) > 0:
 833                         self.workflow_eval_lock.wait(3)
 834                     else:
 835                         logger.error("Workflow is deadlocked, no runnable processes and not waiting on any pending processes.")
 836                         break
 837
 838                 if self.stop_polling.is_set():
 839                     break
 840
 841                 loopperf.__enter__()
 842             loopperf.__exit__()
 843
 844             while (self.task_queue.in_flight + len(self.processes)) > 0:
 845                 if self.task_queue.error is not None:
 846                     raise self.task_queue.error
 847                 self.workflow_eval_lock.wait(3)
 848
 849         except UnsupportedRequirement:
 850             raise
 851         except:
 852             if sys.exc_info()[0] is KeyboardInterrupt or sys.exc_info()[0] is SystemExit:
 853                 logger.error("Interrupted, workflow will be cancelled")
 854             elif isinstance(sys.exc_info()[1], WorkflowException):
 855                 logger.error("Workflow execution failed:\n%s", sys.exc_info()[1], exc_info=(sys.exc_info()[1] if self.debug else False))
 856             else:
 857                 logger.exception("Workflow execution failed")
 858
 859             if self.pipeline:
 860                 self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
 861                                                      body={"state": "Failed"}).execute(num_retries=self.num_retries)
 862
 863             if self.work_api == "containers" and not current_container:
 864                 # Not running in a crunch container, so cancel any outstanding processes.
 865                 for p in self.processes:
 866                     try:
 867                         self.api.container_requests().update(uuid=p,
 868                                                              body={"priority": "0"}
 869                         ).execute(num_retries=self.num_retries)
 870                     except Exception:
 871                         pass
 872         finally:
 873             self.workflow_eval_lock.release()
 874             self.task_queue.drain()
 875             self.stop_polling.set()
 876             self.polling_thread.join()
 877             self.task_queue.join()
 878
 879         if self.final_status == "UnsupportedRequirement":
 880             raise UnsupportedRequirement("Check log for details.")
 881
 882         if self.final_output is None:
 883             raise WorkflowException("Workflow did not return a result.")
 884
 885         if runtimeContext.submit and isinstance(tool, Runner):
 886             logger.info("Final output collection %s", tool.final_output)
 887             if workbench2 or workbench1:
 888                 logger.info("Output at %scollections/%s", workbench2 or workbench1, tool.final_output)
 889         else:
 890             if self.output_tags is None:
 891                 self.output_tags = ""
 892
 893             storage_classes = ""
 894             storage_class_req, _ = tool.get_requirement("http://arvados.org/cwl#OutputStorageClass")
 895             if storage_class_req and storage_class_req.get("finalStorageClass"):
 896                 storage_classes = aslist(storage_class_req["finalStorageClass"])
 897             else:
 898                 storage_classes = runtimeContext.storage_classes.strip().split(",")
 899
 900             output_properties = {}
 901             output_properties_req, _ = tool.get_requirement("http://arvados.org/cwl#OutputCollectionProperties")
 902             if output_properties_req:
 903                 builder = make_builder(job_order, tool.hints, tool.requirements, runtimeContext, tool.metadata)
 904                 for pr in output_properties_req["outputProperties"]:
 905                     output_properties[pr["propertyName"]] = builder.do_eval(pr["propertyValue"])
 906
 907             self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, storage_classes,
 908                                                                                           self.output_tags, output_properties,
 909                                                                                           self.final_output)
 910             self.set_crunch_output()
 911
 912         if runtimeContext.compute_checksum:
 913             adjustDirObjs(self.final_output, partial(get_listing, self.fs_access))
 914             adjustFileObjs(self.final_output, partial(compute_checksums, self.fs_access))
 915
 916         if self.trash_intermediate and self.final_status == "success":
 917             self.trash_intermediate_output()
 918
 919         return (self.final_output, self.final_status)