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.toplevel_runtimeContext = ArvRuntimeContext(vars(arvargs))
201 self.toplevel_runtimeContext.make_fs_access = partial(CollectionFsAccess,
202 collection_cache=self.collection_cache)
204 validate_cluster_target(self, self.toplevel_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)
521 self.fs_access = runtimeContext.make_fs_access(runtimeContext.basedir)
522 self.secret_store = runtimeContext.secret_store
524 self.trash_intermediate = runtimeContext.trash_intermediate
525 if self.trash_intermediate and self.work_api != "containers":
526 raise Exception("--trash-intermediate is only supported with --api=containers.")
528 self.intermediate_output_ttl = runtimeContext.intermediate_output_ttl
529 if self.intermediate_output_ttl and self.work_api != "containers":
530 raise Exception("--intermediate-output-ttl is only supported with --api=containers.")
531 if self.intermediate_output_ttl < 0:
532 raise Exception("Invalid value %d for --intermediate-output-ttl, cannot be less than zero" % self.intermediate_output_ttl)
534 if runtimeContext.submit_request_uuid and self.work_api != "containers":
535 raise Exception("--submit-request-uuid requires containers API, but using '{}' api".format(self.work_api))
537 runtimeContext = runtimeContext.copy()
539 default_storage_classes = ",".join([k for k,v in self.api.config().get("StorageClasses", {"default": {"Default": True}}).items() if v.get("Default") is True])
540 if runtimeContext.storage_classes == "default":
541 runtimeContext.storage_classes = default_storage_classes
542 if runtimeContext.intermediate_storage_classes == "default":
543 runtimeContext.intermediate_storage_classes = default_storage_classes
545 if not runtimeContext.name:
546 runtimeContext.name = self.name = updated_tool.tool.get("label") or updated_tool.metadata.get("label") or os.path.basename(updated_tool.tool["id"])
548 if runtimeContext.copy_deps is None and (runtimeContext.create_workflow or runtimeContext.update_workflow):
549 # When creating or updating workflow record, by default
550 # always copy dependencies and ensure Docker images are up
552 runtimeContext.copy_deps = True
553 runtimeContext.match_local_docker = True
555 if runtimeContext.update_workflow and self.project_uuid is None:
556 # If we are updating a workflow, make sure anything that
557 # gets uploaded goes into the same parent project, unless
558 # an alternate --project-uuid was provided.
559 existing_wf = self.api.workflows().get(uuid=runtimeContext.update_workflow).execute()
560 runtimeContext.project_uuid = existing_wf["owner_uuid"]
562 self.project_uuid = runtimeContext.project_uuid
564 # Upload local file references in the job order.
565 job_order = upload_job_order(self, "%s input" % runtimeContext.name,
566 updated_tool, job_order, runtimeContext)
568 # the last clause means: if it is a command line tool, and we
569 # are going to wait for the result, and always_submit_runner
570 # is false, then we don't submit a runner process.
572 submitting = (runtimeContext.update_workflow or
573 runtimeContext.create_workflow or
574 (runtimeContext.submit and not
575 (updated_tool.tool["class"] == "CommandLineTool" and
576 runtimeContext.wait and
577 not runtimeContext.always_submit_runner)))
579 loadingContext = self.loadingContext.copy()
580 loadingContext.do_validate = False
582 loadingContext.do_update = False
583 # Document may have been auto-updated. Reload the original
584 # document with updating disabled because we want to
585 # submit the document with its original CWL version, not
586 # the auto-updated one.
587 tool = load_tool(updated_tool.tool["id"], loadingContext)
591 # Upload direct dependencies of workflow steps, get back mapping of files to keep references.
592 # Also uploads docker images.
593 merged_map = upload_workflow_deps(self, tool, runtimeContext)
595 # Recreate process object (ArvadosWorkflow or
596 # ArvadosCommandTool) because tool document may have been
597 # updated by upload_workflow_deps in ways that modify
598 # inheritance of hints or requirements.
599 loadingContext.loader = tool.doc_loader
600 loadingContext.avsc_names = tool.doc_schema
601 loadingContext.metadata = tool.metadata
602 tool = load_tool(tool.tool, loadingContext)
604 if runtimeContext.update_workflow or runtimeContext.create_workflow:
605 # Create a pipeline template or workflow record and exit.
606 if self.work_api == "containers":
607 uuid = upload_workflow(self, tool, job_order,
608 runtimeContext.project_uuid,
610 uuid=runtimeContext.update_workflow,
611 submit_runner_ram=runtimeContext.submit_runner_ram,
612 name=runtimeContext.name,
613 merged_map=merged_map,
614 submit_runner_image=runtimeContext.submit_runner_image)
615 self.stdout.write(uuid + "\n")
616 return (None, "success")
618 self.apply_reqs(job_order, tool)
620 self.ignore_docker_for_reuse = runtimeContext.ignore_docker_for_reuse
621 self.eval_timeout = runtimeContext.eval_timeout
623 runtimeContext.use_container = True
624 runtimeContext.tmpdir_prefix = "tmp"
625 runtimeContext.work_api = self.work_api
627 if self.work_api == "containers":
628 if self.ignore_docker_for_reuse:
629 raise Exception("--ignore-docker-for-reuse not supported with containers API.")
630 runtimeContext.outdir = "/var/spool/cwl"
631 runtimeContext.docker_outdir = "/var/spool/cwl"
632 runtimeContext.tmpdir = "/tmp"
633 runtimeContext.docker_tmpdir = "/tmp"
635 if runtimeContext.priority < 1 or runtimeContext.priority > 1000:
636 raise Exception("--priority must be in the range 1..1000.")
638 if self.should_estimate_cache_size:
641 def estimate_collection_cache(obj):
642 if obj.get("location", "").startswith("keep:"):
643 m = pdh_size.match(obj["location"][5:])
644 if m and m.group(1) not in visited:
645 visited.add(m.group(1))
646 estimated_size[0] += int(m.group(2))
647 visit_class(job_order, ("File", "Directory"), estimate_collection_cache)
648 runtimeContext.collection_cache_size = max(((estimated_size[0]*192) // (1024*1024))+1, 256)
649 self.collection_cache.set_cap(runtimeContext.collection_cache_size*1024*1024)
651 logger.info("Using collection cache size %s MiB", runtimeContext.collection_cache_size)
654 if runtimeContext.submit:
655 # Submit a runner job to run the workflow for us.
656 if self.work_api == "containers":
658 tool = RunnerContainer(self, updated_tool,
659 tool, loadingContext, runtimeContext.enable_reuse,
662 submit_runner_ram=runtimeContext.submit_runner_ram,
663 name=runtimeContext.name,
664 on_error=runtimeContext.on_error,
665 submit_runner_image=runtimeContext.submit_runner_image,
666 intermediate_output_ttl=runtimeContext.intermediate_output_ttl,
667 merged_map=merged_map,
668 priority=runtimeContext.priority,
669 secret_store=self.secret_store,
670 collection_cache_size=runtimeContext.collection_cache_size,
671 collection_cache_is_default=self.should_estimate_cache_size)
673 runtimeContext.runnerjob = tool.tool["id"]
675 if runtimeContext.cwl_runner_job is not None:
676 self.uuid = runtimeContext.cwl_runner_job.get('uuid')
678 jobiter = tool.job(job_order,
679 self.output_callback,
682 if runtimeContext.submit and not runtimeContext.wait:
683 runnerjob = next(jobiter)
684 runnerjob.run(runtimeContext)
685 self.stdout.write(runnerjob.uuid+"\n")
686 return (None, "success")
688 current_container = arvados_cwl.util.get_current_container(self.api, self.num_retries, logger)
689 if current_container:
690 logger.info("Running inside container %s", current_container.get("uuid"))
692 self.poll_api = arvados.api('v1', timeout=runtimeContext.http_timeout)
693 self.polling_thread = threading.Thread(target=self.poll_states)
694 self.polling_thread.start()
696 self.task_queue = TaskQueue(self.workflow_eval_lock, self.thread_count)
699 self.workflow_eval_lock.acquire()
701 # Holds the lock while this code runs and releases it when
702 # it is safe to do so in self.workflow_eval_lock.wait(),
703 # at which point on_message can update job state and
704 # process output callbacks.
706 loopperf = Perf(metrics, "jobiter")
708 for runnable in jobiter:
711 if self.stop_polling.is_set():
714 if self.task_queue.error is not None:
715 raise self.task_queue.error
718 with Perf(metrics, "run"):
719 self.start_run(runnable, runtimeContext)
721 if (self.task_queue.in_flight + len(self.processes)) > 0:
722 self.workflow_eval_lock.wait(3)
724 logger.error("Workflow is deadlocked, no runnable processes and not waiting on any pending processes.")
727 if self.stop_polling.is_set():
733 while (self.task_queue.in_flight + len(self.processes)) > 0:
734 if self.task_queue.error is not None:
735 raise self.task_queue.error
736 self.workflow_eval_lock.wait(3)
738 except UnsupportedRequirement:
741 if sys.exc_info()[0] is KeyboardInterrupt or sys.exc_info()[0] is SystemExit:
742 logger.error("Interrupted, workflow will be cancelled")
743 elif isinstance(sys.exc_info()[1], WorkflowException):
744 logger.error("Workflow execution failed:\n%s", sys.exc_info()[1], exc_info=(sys.exc_info()[1] if self.debug else False))
746 logger.exception("Workflow execution failed")
749 self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
750 body={"state": "Failed"}).execute(num_retries=self.num_retries)
752 if self.work_api == "containers" and not current_container:
753 # Not running in a crunch container, so cancel any outstanding processes.
754 for p in self.processes:
756 self.api.container_requests().update(uuid=p,
757 body={"priority": "0"}
758 ).execute(num_retries=self.num_retries)
762 self.workflow_eval_lock.release()
763 self.task_queue.drain()
764 self.stop_polling.set()
765 self.polling_thread.join()
766 self.task_queue.join()
768 if self.final_status == "UnsupportedRequirement":
769 raise UnsupportedRequirement("Check log for details.")
771 if self.final_output is None:
772 raise WorkflowException("Workflow did not return a result.")
774 if runtimeContext.submit and isinstance(tool, Runner):
775 logger.info("Final output collection %s", tool.final_output)
776 if workbench2 or workbench1:
777 logger.info("Output at %scollections/%s", workbench2 or workbench1, tool.final_output)
779 if self.output_name is None:
780 self.output_name = "Output of %s" % (shortname(tool.tool["id"]))
781 if self.output_tags is None:
782 self.output_tags = ""
785 storage_class_req, _ = tool.get_requirement("http://arvados.org/cwl#OutputStorageClass")
786 if storage_class_req and storage_class_req.get("finalStorageClass"):
787 storage_classes = aslist(storage_class_req["finalStorageClass"])
789 storage_classes = runtimeContext.storage_classes.strip().split(",")
791 self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, storage_classes, self.output_tags, self.final_output)
792 self.set_crunch_output()
794 if runtimeContext.compute_checksum:
795 adjustDirObjs(self.final_output, partial(get_listing, self.fs_access))
796 adjustFileObjs(self.final_output, partial(compute_checksums, self.fs_access))
798 if self.trash_intermediate and self.final_status == "success":
799 self.trash_intermediate_output()
801 return (self.final_output, self.final_status)