1 # Copyright (C) The Arvados Authors. All rights reserved.
3 # SPDX-License-Identifier: Apache-2.0
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
19 from functools import partial
23 from cwltool.errors import WorkflowException
24 import cwltool.workflow
25 from schema_salad.sourceline import SourceLine
26 import schema_salad.validate as validate
30 from arvados.keep import KeepClient
31 from arvados.errors import ApiError
33 import arvados_cwl.util
34 from .arvcontainer import RunnerContainer
35 from .runner import Runner, upload_docker, upload_job_order, upload_workflow_deps
36 from .arvtool import ArvadosCommandTool, validate_cluster_target, ArvadosExpressionTool
37 from .arvworkflow import ArvadosWorkflow, upload_workflow
38 from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver, CollectionCache, pdh_size
39 from .perf import Perf
40 from .pathmapper import NoFollowPathMapper
41 from cwltool.task_queue import TaskQueue
42 from .context import ArvLoadingContext, ArvRuntimeContext
43 from ._version import __version__
45 from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema
46 from cwltool.utils import adjustFileObjs, adjustDirObjs, get_listing, visit_class, aslist
47 from cwltool.command_line_tool import compute_checksums
48 from cwltool.load_tool import load_tool
50 logger = logging.getLogger('arvados.cwl-runner')
51 metrics = logging.getLogger('arvados.cwl-runner.metrics')
53 DEFAULT_PRIORITY = 500
55 class RuntimeStatusLoggingHandler(logging.Handler):
57 Intercepts logging calls and report them as runtime statuses on runner
60 def __init__(self, runtime_status_update_func):
61 super(RuntimeStatusLoggingHandler, self).__init__()
62 self.runtime_status_update = runtime_status_update_func
63 self.updatingRuntimeStatus = False
65 def emit(self, record):
67 if record.levelno >= logging.ERROR:
69 elif record.levelno >= logging.WARNING:
71 if kind is not None and self.updatingRuntimeStatus is not True:
72 self.updatingRuntimeStatus = True
74 log_msg = record.getMessage()
76 # If the logged message is multi-line, use its first line as status
77 # and the rest as detail.
78 status, detail = log_msg.split('\n', 1)
79 self.runtime_status_update(
81 "%s: %s" % (record.name, status),
85 self.runtime_status_update(
87 "%s: %s" % (record.name, record.getMessage())
90 self.updatingRuntimeStatus = False
93 class ArvCwlExecutor(object):
94 """Execute a CWL tool or workflow, submit work (using containers API),
95 wait for them to complete, and report output.
99 def __init__(self, api_client,
107 arvargs = argparse.Namespace()
108 arvargs.work_api = None
109 arvargs.output_name = None
110 arvargs.output_tags = None
111 arvargs.thread_count = 1
112 arvargs.collection_cache_size = None
114 self.api = api_client
116 self.workflow_eval_lock = threading.Condition(threading.RLock())
117 self.final_output = None
118 self.final_status = None
119 self.num_retries = num_retries
121 self.stop_polling = threading.Event()
124 self.final_output_collection = None
125 self.output_name = arvargs.output_name
126 self.output_tags = arvargs.output_tags
127 self.project_uuid = None
128 self.intermediate_output_ttl = 0
129 self.intermediate_output_collections = []
130 self.trash_intermediate = False
131 self.thread_count = arvargs.thread_count
132 self.poll_interval = 12
133 self.loadingContext = None
134 self.should_estimate_cache_size = True
135 self.fs_access = None
136 self.secret_store = None
139 if keep_client is not None:
140 self.keep_client = keep_client
142 self.keep_client = arvados.keep.KeepClient(api_client=self.api, num_retries=self.num_retries)
144 if arvargs.collection_cache_size:
145 collection_cache_size = arvargs.collection_cache_size*1024*1024
146 self.should_estimate_cache_size = False
148 collection_cache_size = 256*1024*1024
150 self.collection_cache = CollectionCache(self.api, self.keep_client, self.num_retries,
151 cap=collection_cache_size)
153 self.fetcher_constructor = partial(CollectionFetcher,
155 fs_access=CollectionFsAccess("", collection_cache=self.collection_cache),
156 num_retries=self.num_retries)
159 expected_api = ["containers"]
160 for api in expected_api:
162 methods = self.api._rootDesc.get('resources')[api]['methods']
163 if ('httpMethod' in methods['create'] and
164 (arvargs.work_api == api or arvargs.work_api is None)):
170 if not self.work_api:
171 if arvargs.work_api is None:
172 raise Exception("No supported APIs")
174 raise Exception("Unsupported API '%s', expected one of %s" % (arvargs.work_api, expected_api))
176 if self.work_api == "jobs":
178 *******************************
179 The 'jobs' API is no longer supported.
180 *******************************""")
183 self.loadingContext = ArvLoadingContext(vars(arvargs))
184 self.loadingContext.fetcher_constructor = self.fetcher_constructor
185 self.loadingContext.resolver = partial(collectionResolver, self.api, num_retries=self.num_retries)
186 self.loadingContext.construct_tool_object = self.arv_make_tool
188 # Add a custom logging handler to the root logger for runtime status reporting
189 # if running inside a container
190 if arvados_cwl.util.get_current_container(self.api, self.num_retries, logger):
191 root_logger = logging.getLogger('')
193 # Remove existing RuntimeStatusLoggingHandlers if they exist
194 handlers = [h for h in root_logger.handlers if not isinstance(h, RuntimeStatusLoggingHandler)]
195 root_logger.handlers = handlers
197 handler = RuntimeStatusLoggingHandler(self.runtime_status_update)
198 root_logger.addHandler(handler)
200 self.runtimeContext = ArvRuntimeContext(vars(arvargs))
201 self.runtimeContext.make_fs_access = partial(CollectionFsAccess,
202 collection_cache=self.collection_cache)
204 validate_cluster_target(self, self.runtimeContext)
207 def arv_make_tool(self, toolpath_object, loadingContext):
208 if "class" in toolpath_object and toolpath_object["class"] == "CommandLineTool":
209 return ArvadosCommandTool(self, toolpath_object, loadingContext)
210 elif "class" in toolpath_object and toolpath_object["class"] == "Workflow":
211 return ArvadosWorkflow(self, toolpath_object, loadingContext)
212 elif "class" in toolpath_object and toolpath_object["class"] == "ExpressionTool":
213 return ArvadosExpressionTool(self, toolpath_object, loadingContext)
215 raise Exception("Unknown tool %s" % toolpath_object.get("class"))
217 def output_callback(self, out, processStatus):
218 with self.workflow_eval_lock:
219 if processStatus == "success":
220 logger.info("Overall process status is %s", processStatus)
223 logger.error("Overall process status is %s", processStatus)
226 self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
227 body={"state": state}).execute(num_retries=self.num_retries)
228 self.final_status = processStatus
229 self.final_output = out
230 self.workflow_eval_lock.notifyAll()
233 def start_run(self, runnable, runtimeContext):
234 self.task_queue.add(partial(runnable.run, runtimeContext),
235 self.workflow_eval_lock, self.stop_polling)
237 def process_submitted(self, container):
238 with self.workflow_eval_lock:
239 self.processes[container.uuid] = container
241 def process_done(self, uuid, record):
242 with self.workflow_eval_lock:
243 j = self.processes[uuid]
244 logger.info("%s %s is %s", self.label(j), uuid, record["state"])
245 self.task_queue.add(partial(j.done, record),
246 self.workflow_eval_lock, self.stop_polling)
247 del self.processes[uuid]
249 def runtime_status_update(self, kind, message, detail=None):
251 Updates the runtime_status field on the runner container.
252 Called when there's a need to report errors, warnings or just
253 activity statuses, for example in the RuntimeStatusLoggingHandler.
255 with self.workflow_eval_lock:
258 current = arvados_cwl.util.get_current_container(self.api, self.num_retries, logger)
259 except Exception as e:
260 logger.info("Couldn't get current container: %s", e)
263 runtime_status = current.get('runtime_status', {})
264 if kind in ('error', 'warning'):
265 updatemessage = runtime_status.get(kind, "")
266 if not updatemessage:
267 updatemessage = message
269 # Subsequent messages tacked on in detail
270 updatedetail = runtime_status.get(kind+'Detail', "")
272 if updatedetail.count("\n") < maxlines:
275 updatedetail += message + "\n"
278 updatedetail += detail + "\n"
280 if updatedetail.count("\n") >= maxlines:
281 updatedetail += "\nSome messages may have been omitted. Check the full log."
283 runtime_status.update({
285 kind+'Detail': updatedetail,
288 # Ignore any other status kind
291 self.api.containers().update(uuid=current['uuid'],
293 'runtime_status': runtime_status,
294 }).execute(num_retries=self.num_retries)
295 except Exception as e:
296 logger.info("Couldn't update runtime_status: %s", e)
298 def wrapped_callback(self, cb, obj, st):
299 with self.workflow_eval_lock:
301 self.workflow_eval_lock.notifyAll()
303 def get_wrapped_callback(self, cb):
304 return partial(self.wrapped_callback, cb)
306 def on_message(self, event):
307 if event.get("object_uuid") in self.processes and event["event_type"] == "update":
308 uuid = event["object_uuid"]
309 if event["properties"]["new_attributes"]["state"] == "Running":
310 with self.workflow_eval_lock:
311 j = self.processes[uuid]
312 if j.running is False:
314 j.update_pipeline_component(event["properties"]["new_attributes"])
315 logger.info("%s %s is Running", self.label(j), uuid)
316 elif event["properties"]["new_attributes"]["state"] in ("Complete", "Failed", "Cancelled", "Final"):
317 self.process_done(uuid, event["properties"]["new_attributes"])
319 def label(self, obj):
320 return "[%s %s]" % (self.work_api[0:-1], obj.name)
322 def poll_states(self):
323 """Poll status of containers listed in the processes dict.
325 Runs in a separate thread.
329 remain_wait = self.poll_interval
332 self.stop_polling.wait(remain_wait)
333 if self.stop_polling.is_set():
335 with self.workflow_eval_lock:
336 keys = list(self.processes)
338 remain_wait = self.poll_interval
341 begin_poll = time.time()
342 if self.work_api == "containers":
343 table = self.poll_api.container_requests()
345 pageSize = self.poll_api._rootDesc.get('maxItemsPerResponse', 1000)
348 page = keys[:pageSize]
350 proc_states = table.list(filters=[["uuid", "in", page]]).execute(num_retries=self.num_retries)
352 logger.exception("Error checking states on API server: %s")
353 remain_wait = self.poll_interval
356 for p in proc_states["items"]:
358 "object_uuid": p["uuid"],
359 "event_type": "update",
364 keys = keys[pageSize:]
366 finish_poll = time.time()
367 remain_wait = self.poll_interval - (finish_poll - begin_poll)
369 logger.exception("Fatal error in state polling thread.")
370 with self.workflow_eval_lock:
371 self.processes.clear()
372 self.workflow_eval_lock.notifyAll()
374 self.stop_polling.set()
376 def add_intermediate_output(self, uuid):
378 self.intermediate_output_collections.append(uuid)
380 def trash_intermediate_output(self):
381 logger.info("Cleaning up intermediate output collections")
382 for i in self.intermediate_output_collections:
384 self.api.collections().delete(uuid=i).execute(num_retries=self.num_retries)
386 logger.warning("Failed to delete intermediate output: %s", sys.exc_info()[1], exc_info=(sys.exc_info()[1] if self.debug else False))
387 except (KeyboardInterrupt, SystemExit):
390 def check_features(self, obj, parentfield=""):
391 if isinstance(obj, dict):
392 if obj.get("class") == "DockerRequirement":
393 if obj.get("dockerOutputDirectory"):
394 if not obj.get("dockerOutputDirectory").startswith('/'):
395 raise SourceLine(obj, "dockerOutputDirectory", validate.ValidationException).makeError(
396 "Option 'dockerOutputDirectory' must be an absolute path.")
397 if obj.get("class") == "InplaceUpdateRequirement":
398 if obj["inplaceUpdate"] and parentfield == "requirements":
399 raise SourceLine(obj, "class", UnsupportedRequirement).makeError("InplaceUpdateRequirement not supported for keep collections.")
400 for k,v in viewitems(obj):
401 self.check_features(v, parentfield=k)
402 elif isinstance(obj, list):
403 for i,v in enumerate(obj):
404 with SourceLine(obj, i, UnsupportedRequirement, logger.isEnabledFor(logging.DEBUG)):
405 self.check_features(v, parentfield=parentfield)
407 def make_output_collection(self, name, storage_classes, tagsString, outputObj):
408 outputObj = copy.deepcopy(outputObj)
411 def capture(fileobj):
412 files.append(fileobj)
414 adjustDirObjs(outputObj, capture)
415 adjustFileObjs(outputObj, capture)
417 generatemapper = NoFollowPathMapper(files, "", "", separateDirs=False)
419 final = arvados.collection.Collection(api_client=self.api,
420 keep_client=self.keep_client,
421 num_retries=self.num_retries)
423 for k,v in generatemapper.items():
424 if v.type == "Directory" and v.resolved.startswith("_:"):
426 if v.type == "CreateFile" and (k.startswith("_:") or v.resolved.startswith("_:")):
427 with final.open(v.target, "wb") as f:
428 f.write(v.resolved.encode("utf-8"))
431 if not v.resolved.startswith("keep:"):
432 raise Exception("Output source is not in keep or a literal")
433 sp = v.resolved.split("/")
434 srccollection = sp[0][5:]
436 reader = self.collection_cache.get(srccollection)
437 srcpath = urllib.parse.unquote("/".join(sp[1:]) if len(sp) > 1 else ".")
438 final.copy(srcpath, v.target, source_collection=reader, overwrite=False)
439 except arvados.errors.ArgumentError as e:
440 logger.error("Creating CollectionReader for '%s' '%s': %s", k, v, e)
443 logger.error("While preparing output collection: %s", e)
446 def rewrite(fileobj):
447 fileobj["location"] = generatemapper.mapper(fileobj["location"]).target
448 for k in ("listing", "contents", "nameext", "nameroot", "dirname"):
452 adjustDirObjs(outputObj, rewrite)
453 adjustFileObjs(outputObj, rewrite)
455 with final.open("cwl.output.json", "w") as f:
456 res = str(json.dumps(outputObj, sort_keys=True, indent=4, separators=(',',': '), ensure_ascii=False))
459 final.save_new(name=name, owner_uuid=self.project_uuid, storage_classes=storage_classes, ensure_unique_name=True)
461 logger.info("Final output collection %s \"%s\" (%s)", final.portable_data_hash(),
462 final.api_response()["name"],
463 final.manifest_locator())
465 final_uuid = final.manifest_locator()
466 tags = tagsString.split(',')
468 self.api.links().create(body={
469 "head_uuid": final_uuid, "link_class": "tag", "name": tag
470 }).execute(num_retries=self.num_retries)
472 def finalcollection(fileobj):
473 fileobj["location"] = "keep:%s/%s" % (final.portable_data_hash(), fileobj["location"])
475 adjustDirObjs(outputObj, finalcollection)
476 adjustFileObjs(outputObj, finalcollection)
478 return (outputObj, final)
480 def set_crunch_output(self):
481 if self.work_api == "containers":
482 current = arvados_cwl.util.get_current_container(self.api, self.num_retries, logger)
486 self.api.containers().update(uuid=current['uuid'],
488 'output': self.final_output_collection.portable_data_hash(),
489 }).execute(num_retries=self.num_retries)
490 self.api.collections().update(uuid=self.final_output_collection.manifest_locator(),
493 }).execute(num_retries=self.num_retries)
495 logger.exception("Setting container output")
498 def apply_reqs(self, job_order_object, tool):
499 if "https://w3id.org/cwl/cwl#requirements" in job_order_object:
500 if tool.metadata.get("http://commonwl.org/cwltool#original_cwlVersion") == 'v1.0':
501 raise WorkflowException(
502 "`cwl:requirements` in the input object is not part of CWL "
503 "v1.0. You can adjust to use `cwltool:overrides` instead; or you "
504 "can set the cwlVersion to v1.1 or greater and re-run with "
506 job_reqs = job_order_object["https://w3id.org/cwl/cwl#requirements"]
508 tool.requirements.append(req)
510 def arv_executor(self, updated_tool, job_order, runtimeContext, logger=None):
511 self.debug = runtimeContext.debug
513 workbench1 = self.api.config()["Services"]["Workbench1"]["ExternalURL"]
514 workbench2 = self.api.config()["Services"]["Workbench2"]["ExternalURL"]
515 controller = self.api.config()["Services"]["Controller"]["ExternalURL"]
516 logger.info("Using cluster %s (%s)", self.api.config()["ClusterID"], workbench2 or workbench1 or controller)
518 updated_tool.visit(self.check_features)
520 self.project_uuid = runtimeContext.project_uuid
522 self.fs_access = runtimeContext.make_fs_access(runtimeContext.basedir)
523 self.secret_store = runtimeContext.secret_store
525 self.trash_intermediate = runtimeContext.trash_intermediate
526 if self.trash_intermediate and self.work_api != "containers":
527 raise Exception("--trash-intermediate is only supported with --api=containers.")
529 self.intermediate_output_ttl = runtimeContext.intermediate_output_ttl
530 if self.intermediate_output_ttl and self.work_api != "containers":
531 raise Exception("--intermediate-output-ttl is only supported with --api=containers.")
532 if self.intermediate_output_ttl < 0:
533 raise Exception("Invalid value %d for --intermediate-output-ttl, cannot be less than zero" % self.intermediate_output_ttl)
535 if runtimeContext.submit_request_uuid and self.work_api != "containers":
536 raise Exception("--submit-request-uuid requires containers API, but using '{}' api".format(self.work_api))
538 default_storage_classes = ",".join([k for k,v in self.api.config().get("StorageClasses", {"default": {"Default": True}}).items() if v.get("Default") is True])
539 if runtimeContext.storage_classes == "default":
540 runtimeContext.storage_classes = default_storage_classes
541 if runtimeContext.intermediate_storage_classes == "default":
542 runtimeContext.intermediate_storage_classes = default_storage_classes
544 if not runtimeContext.name:
545 runtimeContext.name = self.name = updated_tool.tool.get("label") or updated_tool.metadata.get("label") or os.path.basename(updated_tool.tool["id"])
547 # Upload local file references in the job order.
548 job_order = upload_job_order(self, "%s input" % runtimeContext.name,
549 updated_tool, job_order)
551 # the last clause means: if it is a command line tool, and we
552 # are going to wait for the result, and always_submit_runner
553 # is false, then we don't submit a runner process.
555 submitting = (runtimeContext.update_workflow or
556 runtimeContext.create_workflow or
557 (runtimeContext.submit and not
558 (updated_tool.tool["class"] == "CommandLineTool" and
559 runtimeContext.wait and
560 not runtimeContext.always_submit_runner)))
562 loadingContext = self.loadingContext.copy()
563 loadingContext.do_validate = False
565 loadingContext.do_update = False
566 # Document may have been auto-updated. Reload the original
567 # document with updating disabled because we want to
568 # submit the document with its original CWL version, not
569 # the auto-updated one.
570 tool = load_tool(updated_tool.tool["id"], loadingContext)
574 # Upload direct dependencies of workflow steps, get back mapping of files to keep references.
575 # Also uploads docker images.
576 merged_map = upload_workflow_deps(self, tool)
578 # Recreate process object (ArvadosWorkflow or
579 # ArvadosCommandTool) because tool document may have been
580 # updated by upload_workflow_deps in ways that modify
581 # inheritance of hints or requirements.
582 loadingContext.loader = tool.doc_loader
583 loadingContext.avsc_names = tool.doc_schema
584 loadingContext.metadata = tool.metadata
585 tool = load_tool(tool.tool, loadingContext)
587 existing_uuid = runtimeContext.update_workflow
588 if existing_uuid or runtimeContext.create_workflow:
589 # Create a pipeline template or workflow record and exit.
590 if self.work_api == "containers":
591 uuid = upload_workflow(self, tool, job_order,
594 submit_runner_ram=runtimeContext.submit_runner_ram,
595 name=runtimeContext.name,
596 merged_map=merged_map,
597 submit_runner_image=runtimeContext.submit_runner_image)
598 self.stdout.write(uuid + "\n")
599 return (None, "success")
601 self.apply_reqs(job_order, tool)
603 self.ignore_docker_for_reuse = runtimeContext.ignore_docker_for_reuse
604 self.eval_timeout = runtimeContext.eval_timeout
606 runtimeContext = runtimeContext.copy()
607 runtimeContext.use_container = True
608 runtimeContext.tmpdir_prefix = "tmp"
609 runtimeContext.work_api = self.work_api
611 if self.work_api == "containers":
612 if self.ignore_docker_for_reuse:
613 raise Exception("--ignore-docker-for-reuse not supported with containers API.")
614 runtimeContext.outdir = "/var/spool/cwl"
615 runtimeContext.docker_outdir = "/var/spool/cwl"
616 runtimeContext.tmpdir = "/tmp"
617 runtimeContext.docker_tmpdir = "/tmp"
619 if runtimeContext.priority < 1 or runtimeContext.priority > 1000:
620 raise Exception("--priority must be in the range 1..1000.")
622 if self.should_estimate_cache_size:
625 def estimate_collection_cache(obj):
626 if obj.get("location", "").startswith("keep:"):
627 m = pdh_size.match(obj["location"][5:])
628 if m and m.group(1) not in visited:
629 visited.add(m.group(1))
630 estimated_size[0] += int(m.group(2))
631 visit_class(job_order, ("File", "Directory"), estimate_collection_cache)
632 runtimeContext.collection_cache_size = max(((estimated_size[0]*192) // (1024*1024))+1, 256)
633 self.collection_cache.set_cap(runtimeContext.collection_cache_size*1024*1024)
635 logger.info("Using collection cache size %s MiB", runtimeContext.collection_cache_size)
638 if runtimeContext.submit:
639 # Submit a runner job to run the workflow for us.
640 if self.work_api == "containers":
642 tool = RunnerContainer(self, updated_tool,
643 tool, loadingContext, runtimeContext.enable_reuse,
646 submit_runner_ram=runtimeContext.submit_runner_ram,
647 name=runtimeContext.name,
648 on_error=runtimeContext.on_error,
649 submit_runner_image=runtimeContext.submit_runner_image,
650 intermediate_output_ttl=runtimeContext.intermediate_output_ttl,
651 merged_map=merged_map,
652 priority=runtimeContext.priority,
653 secret_store=self.secret_store,
654 collection_cache_size=runtimeContext.collection_cache_size,
655 collection_cache_is_default=self.should_estimate_cache_size)
657 runtimeContext.runnerjob = tool.tool["id"]
659 if runtimeContext.cwl_runner_job is not None:
660 self.uuid = runtimeContext.cwl_runner_job.get('uuid')
662 jobiter = tool.job(job_order,
663 self.output_callback,
666 if runtimeContext.submit and not runtimeContext.wait:
667 runnerjob = next(jobiter)
668 runnerjob.run(runtimeContext)
669 self.stdout.write(runnerjob.uuid+"\n")
670 return (None, "success")
672 current_container = arvados_cwl.util.get_current_container(self.api, self.num_retries, logger)
673 if current_container:
674 logger.info("Running inside container %s", current_container.get("uuid"))
676 self.poll_api = arvados.api('v1', timeout=runtimeContext.http_timeout)
677 self.polling_thread = threading.Thread(target=self.poll_states)
678 self.polling_thread.start()
680 self.task_queue = TaskQueue(self.workflow_eval_lock, self.thread_count)
683 self.workflow_eval_lock.acquire()
685 # Holds the lock while this code runs and releases it when
686 # it is safe to do so in self.workflow_eval_lock.wait(),
687 # at which point on_message can update job state and
688 # process output callbacks.
690 loopperf = Perf(metrics, "jobiter")
692 for runnable in jobiter:
695 if self.stop_polling.is_set():
698 if self.task_queue.error is not None:
699 raise self.task_queue.error
702 with Perf(metrics, "run"):
703 self.start_run(runnable, runtimeContext)
705 if (self.task_queue.in_flight + len(self.processes)) > 0:
706 self.workflow_eval_lock.wait(3)
708 logger.error("Workflow is deadlocked, no runnable processes and not waiting on any pending processes.")
711 if self.stop_polling.is_set():
717 while (self.task_queue.in_flight + len(self.processes)) > 0:
718 if self.task_queue.error is not None:
719 raise self.task_queue.error
720 self.workflow_eval_lock.wait(3)
722 except UnsupportedRequirement:
725 if sys.exc_info()[0] is KeyboardInterrupt or sys.exc_info()[0] is SystemExit:
726 logger.error("Interrupted, workflow will be cancelled")
727 elif isinstance(sys.exc_info()[1], WorkflowException):
728 logger.error("Workflow execution failed:\n%s", sys.exc_info()[1], exc_info=(sys.exc_info()[1] if self.debug else False))
730 logger.exception("Workflow execution failed")
733 self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
734 body={"state": "Failed"}).execute(num_retries=self.num_retries)
736 if self.work_api == "containers" and not current_container:
737 # Not running in a crunch container, so cancel any outstanding processes.
738 for p in self.processes:
740 self.api.container_requests().update(uuid=p,
741 body={"priority": "0"}
742 ).execute(num_retries=self.num_retries)
746 self.workflow_eval_lock.release()
747 self.task_queue.drain()
748 self.stop_polling.set()
749 self.polling_thread.join()
750 self.task_queue.join()
752 if self.final_status == "UnsupportedRequirement":
753 raise UnsupportedRequirement("Check log for details.")
755 if self.final_output is None:
756 raise WorkflowException("Workflow did not return a result.")
758 if runtimeContext.submit and isinstance(tool, Runner):
759 logger.info("Final output collection %s", tool.final_output)
760 if workbench2 or workbench1:
761 logger.info("Output at %scollections/%s", workbench2 or workbench1, tool.final_output)
763 if self.output_name is None:
764 self.output_name = "Output of %s" % (shortname(tool.tool["id"]))
765 if self.output_tags is None:
766 self.output_tags = ""
769 storage_class_req, _ = tool.get_requirement("http://arvados.org/cwl#OutputStorageClass")
770 if storage_class_req and storage_class_req.get("finalStorageClass"):
771 storage_classes = aslist(storage_class_req["finalStorageClass"])
773 storage_classes = runtimeContext.storage_classes.strip().split(",")
775 self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, storage_classes, self.output_tags, self.final_output)
776 self.set_crunch_output()
778 if runtimeContext.compute_checksum:
779 adjustDirObjs(self.final_output, partial(get_listing, self.fs_access))
780 adjustFileObjs(self.final_output, partial(compute_checksums, self.fs_access))
782 if self.trash_intermediate and self.final_status == "success":
783 self.trash_intermediate_output()
785 return (self.final_output, self.final_status)