1 # Copyright (C) The Arvados Authors. All rights reserved.
3 # SPDX-License-Identifier: Apache-2.0
5 from future import standard_library
6 standard_library.install_aliases()
7 from builtins import str
12 import urllib.request, urllib.parse, urllib.error
19 import arvados_cwl.util
20 import ruamel.yaml as yaml
22 from cwltool.errors import WorkflowException
23 from cwltool.process import UnsupportedRequirement, shortname
24 from cwltool.utils import aslist, adjustFileObjs, adjustDirObjs, visit_class
25 from cwltool.job import JobBase
27 import arvados.collection
29 from .arvdocker import arv_docker_get_image
31 from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location, remove_redundant_fields, make_builder
32 from .fsaccess import CollectionFetcher
33 from .pathmapper import NoFollowPathMapper, trim_listing
34 from .perf import Perf
35 from ._version import __version__
37 logger = logging.getLogger('arvados.cwl-runner')
38 metrics = logging.getLogger('arvados.cwl-runner.metrics')
40 class ArvadosContainer(JobBase):
41 """Submit and manage a Crunch container request for executing a CWL CommandLineTool."""
43 def __init__(self, runner, job_runtime,
44 builder, # type: Builder
45 joborder, # type: Dict[Text, Union[Dict[Text, Any], List, Text]]
46 make_path_mapper, # type: Callable[..., PathMapper]
47 requirements, # type: List[Dict[Text, Text]]
48 hints, # type: List[Dict[Text, Text]]
51 super(ArvadosContainer, self).__init__(builder, joborder, make_path_mapper, requirements, hints, name)
52 self.arvrunner = runner
53 self.job_runtime = job_runtime
57 def update_pipeline_component(self, r):
60 def run(self, runtimeContext):
61 # ArvadosCommandTool subclasses from cwltool.CommandLineTool,
62 # which calls makeJobRunner() to get a new ArvadosContainer
63 # object. The fields that define execution such as
64 # command_line, environment, etc are set on the
65 # ArvadosContainer object by CommandLineTool.job() before
68 runtimeContext = self.job_runtime
70 if runtimeContext.submit_request_uuid:
71 container_request = self.arvrunner.api.container_requests().get(
72 uuid=runtimeContext.submit_request_uuid
73 ).execute(num_retries=self.arvrunner.num_retries)
75 container_request = {}
77 container_request["command"] = self.command_line
78 container_request["name"] = self.name
79 container_request["output_path"] = self.outdir
80 container_request["cwd"] = self.outdir
81 container_request["priority"] = runtimeContext.priority
82 container_request["state"] = "Committed"
83 container_request.setdefault("properties", {})
85 runtime_constraints = {}
87 if runtimeContext.project_uuid:
88 container_request["owner_uuid"] = runtimeContext.project_uuid
90 if self.arvrunner.secret_store.has_secret(self.command_line):
91 raise WorkflowException("Secret material leaked on command line, only file literals may contain secrets")
93 if self.arvrunner.secret_store.has_secret(self.environment):
94 raise WorkflowException("Secret material leaked in environment, only file literals may contain secrets")
96 resources = self.builder.resources
97 if resources is not None:
98 runtime_constraints["vcpus"] = math.ceil(resources.get("cores", 1))
99 runtime_constraints["ram"] = math.ceil(resources.get("ram") * 2**20)
104 "capacity": math.ceil(resources.get("outdirSize", 0) * 2**20)
108 "capacity": math.ceil(resources.get("tmpdirSize", 0) * 2**20)
112 scheduling_parameters = {}
114 rf = [self.pathmapper.mapper(f) for f in self.pathmapper.referenced_files]
115 rf.sort(key=lambda k: k.resolved)
117 for resolved, target, tp, stg in rf:
120 if prevdir and target.startswith(prevdir):
122 if tp == "Directory":
125 targetdir = os.path.dirname(target)
126 sp = resolved.split("/", 1)
127 pdh = sp[0][5:] # remove "keep:"
128 mounts[targetdir] = {
129 "kind": "collection",
130 "portable_data_hash": pdh
132 if pdh in self.pathmapper.pdh_to_uuid:
133 mounts[targetdir]["uuid"] = self.pathmapper.pdh_to_uuid[pdh]
135 if tp == "Directory":
138 path = os.path.dirname(sp[1])
139 if path and path != "/":
140 mounts[targetdir]["path"] = path
141 prevdir = targetdir + "/"
143 with Perf(metrics, "generatefiles %s" % self.name):
144 if self.generatefiles["listing"]:
145 vwd = arvados.collection.Collection(api_client=self.arvrunner.api,
146 keep_client=self.arvrunner.keep_client,
147 num_retries=self.arvrunner.num_retries)
148 generatemapper = NoFollowPathMapper(self.generatefiles["listing"], "", "",
151 sorteditems = sorted(generatemapper.items(), key=lambda n: n[1].target)
153 logger.debug("generatemapper is %s", sorteditems)
155 with Perf(metrics, "createfiles %s" % self.name):
156 for f, p in sorteditems:
160 if p.target.startswith("/"):
161 dst = p.target[len(self.outdir)+1:] if p.target.startswith(self.outdir+"/") else p.target[1:]
165 if p.type in ("File", "Directory", "WritableFile", "WritableDirectory"):
166 if p.resolved.startswith("_:"):
169 source, path = self.arvrunner.fs_access.get_collection(p.resolved)
170 vwd.copy(path or ".", dst, source_collection=source)
171 elif p.type == "CreateFile":
172 if self.arvrunner.secret_store.has_secret(p.resolved):
173 mountpoint = p.target if p.target.startswith("/") else os.path.join(self.outdir, p.target)
174 secret_mounts[mountpoint] = {
176 "content": self.arvrunner.secret_store.retrieve(p.resolved)
179 with vwd.open(dst, "w") as n:
182 def keepemptydirs(p):
183 if isinstance(p, arvados.collection.RichCollectionBase):
185 p.open(".keep", "w").close()
192 if not runtimeContext.current_container:
193 runtimeContext.current_container = arvados_cwl.util.get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger)
194 info = arvados_cwl.util.get_intermediate_collection_info(self.name, runtimeContext.current_container, runtimeContext.intermediate_output_ttl)
195 vwd.save_new(name=info["name"],
196 owner_uuid=runtimeContext.project_uuid,
197 ensure_unique_name=True,
198 trash_at=info["trash_at"],
199 properties=info["properties"])
202 for f, p in sorteditems:
203 if (not p.target or self.arvrunner.secret_store.has_secret(p.resolved) or
204 (prev is not None and p.target.startswith(prev))):
206 if p.target.startswith("/"):
207 dst = p.target[len(self.outdir)+1:] if p.target.startswith(self.outdir+"/") else p.target[1:]
210 mountpoint = p.target if p.target.startswith("/") else os.path.join(self.outdir, p.target)
211 mounts[mountpoint] = {"kind": "collection",
212 "portable_data_hash": vwd.portable_data_hash(),
214 if p.type.startswith("Writable"):
215 mounts[mountpoint]["writable"] = True
216 prev = p.target + "/"
218 container_request["environment"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
220 container_request["environment"].update(self.environment)
223 sp = self.stdin[6:].split("/", 1)
224 mounts["stdin"] = {"kind": "collection",
225 "portable_data_hash": sp[0],
229 mounts["stderr"] = {"kind": "file",
230 "path": "%s/%s" % (self.outdir, self.stderr)}
233 mounts["stdout"] = {"kind": "file",
234 "path": "%s/%s" % (self.outdir, self.stdout)}
236 (docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
238 docker_req = {"dockerImageId": "arvados/jobs:"+__version__}
240 container_request["container_image"] = arv_docker_get_image(self.arvrunner.api,
242 runtimeContext.pull_image,
243 runtimeContext.project_uuid,
244 runtimeContext.force_docker_pull,
245 runtimeContext.tmp_outdir_prefix)
247 network_req, _ = self.get_requirement("NetworkAccess")
249 runtime_constraints["API"] = network_req["networkAccess"]
251 api_req, _ = self.get_requirement("http://arvados.org/cwl#APIRequirement")
253 runtime_constraints["API"] = True
255 runtime_req, _ = self.get_requirement("http://arvados.org/cwl#RuntimeConstraints")
257 if "keep_cache" in runtime_req:
258 runtime_constraints["keep_cache_ram"] = math.ceil(runtime_req["keep_cache"] * 2**20)
259 if "outputDirType" in runtime_req:
260 if runtime_req["outputDirType"] == "local_output_dir":
261 # Currently the default behavior.
263 elif runtime_req["outputDirType"] == "keep_output_dir":
264 mounts[self.outdir]= {
265 "kind": "collection",
269 partition_req, _ = self.get_requirement("http://arvados.org/cwl#PartitionRequirement")
271 scheduling_parameters["partitions"] = aslist(partition_req["partition"])
273 intermediate_output_req, _ = self.get_requirement("http://arvados.org/cwl#IntermediateOutput")
274 if intermediate_output_req:
275 self.output_ttl = intermediate_output_req["outputTTL"]
277 self.output_ttl = self.arvrunner.intermediate_output_ttl
279 if self.output_ttl < 0:
280 raise WorkflowException("Invalid value %d for output_ttl, cannot be less than zero" % container_request["output_ttl"])
282 storage_class_req, _ = self.get_requirement("http://arvados.org/cwl#OutputStorageClass")
283 if storage_class_req and storage_class_req.get("intermediateStorageClass"):
284 container_request["output_storage_classes"] = aslist(storage_class_req["intermediateStorageClass"])
286 container_request["output_storage_classes"] = runtimeContext.intermediate_storage_classes.strip().split(",")
288 if self.timelimit is not None and self.timelimit > 0:
289 scheduling_parameters["max_run_time"] = self.timelimit
291 extra_submit_params = {}
292 if runtimeContext.submit_runner_cluster:
293 extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster
295 container_request["output_name"] = "Output for step %s" % (self.name)
296 container_request["output_ttl"] = self.output_ttl
297 container_request["mounts"] = mounts
298 container_request["secret_mounts"] = secret_mounts
299 container_request["runtime_constraints"] = runtime_constraints
300 container_request["scheduling_parameters"] = scheduling_parameters
302 enable_reuse = runtimeContext.enable_reuse
304 reuse_req, _ = self.get_requirement("WorkReuse")
306 enable_reuse = reuse_req["enableReuse"]
307 reuse_req, _ = self.get_requirement("http://arvados.org/cwl#ReuseRequirement")
309 enable_reuse = reuse_req["enableReuse"]
310 container_request["use_existing"] = enable_reuse
312 properties_req, _ = self.get_requirement("http://arvados.org/cwl#ProcessProperties")
314 for pr in properties_req["processProperties"]:
315 container_request["properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"])
317 if runtimeContext.runnerjob.startswith("arvwf:"):
318 wfuuid = runtimeContext.runnerjob[6:runtimeContext.runnerjob.index("#")]
319 wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(num_retries=self.arvrunner.num_retries)
320 if container_request["name"] == "main":
321 container_request["name"] = wfrecord["name"]
322 container_request["properties"]["template_uuid"] = wfuuid
324 self.output_callback = self.arvrunner.get_wrapped_callback(self.output_callback)
327 if runtimeContext.submit_request_uuid:
328 response = self.arvrunner.api.container_requests().update(
329 uuid=runtimeContext.submit_request_uuid,
330 body=container_request,
331 **extra_submit_params
332 ).execute(num_retries=self.arvrunner.num_retries)
334 response = self.arvrunner.api.container_requests().create(
335 body=container_request,
336 **extra_submit_params
337 ).execute(num_retries=self.arvrunner.num_retries)
339 self.uuid = response["uuid"]
340 self.arvrunner.process_submitted(self)
342 if response["state"] == "Final":
343 logger.info("%s reused container %s", self.arvrunner.label(self), response["container_uuid"])
345 logger.info("%s %s state is %s", self.arvrunner.label(self), response["uuid"], response["state"])
346 except Exception as e:
347 logger.exception("%s error submitting container\n%s", self.arvrunner.label(self), e)
348 logger.debug("Container request was %s", container_request)
349 self.output_callback({}, "permanentFail")
351 def done(self, record):
354 container = self.arvrunner.api.containers().get(
355 uuid=record["container_uuid"]
356 ).execute(num_retries=self.arvrunner.num_retries)
357 if container["state"] == "Complete":
358 rcode = container["exit_code"]
359 if self.successCodes and rcode in self.successCodes:
360 processStatus = "success"
361 elif self.temporaryFailCodes and rcode in self.temporaryFailCodes:
362 processStatus = "temporaryFail"
363 elif self.permanentFailCodes and rcode in self.permanentFailCodes:
364 processStatus = "permanentFail"
366 processStatus = "success"
368 processStatus = "permanentFail"
370 processStatus = "permanentFail"
372 if processStatus == "permanentFail" and record["log_uuid"]:
373 logc = arvados.collection.CollectionReader(record["log_uuid"],
374 api_client=self.arvrunner.api,
375 keep_client=self.arvrunner.keep_client,
376 num_retries=self.arvrunner.num_retries)
377 label = self.arvrunner.label(self)
380 "%s (%s) error log:" % (label, record["uuid"]), maxlen=40)
382 if record["output_uuid"]:
383 if self.arvrunner.trash_intermediate or self.arvrunner.intermediate_output_ttl:
384 # Compute the trash time to avoid requesting the collection record.
385 trash_at = ciso8601.parse_datetime_as_naive(record["modified_at"]) + datetime.timedelta(0, self.arvrunner.intermediate_output_ttl)
386 aftertime = " at %s" % trash_at.strftime("%Y-%m-%d %H:%M:%S UTC") if self.arvrunner.intermediate_output_ttl else ""
387 orpart = ", or" if self.arvrunner.trash_intermediate and self.arvrunner.intermediate_output_ttl else ""
388 oncomplete = " upon successful completion of the workflow" if self.arvrunner.trash_intermediate else ""
389 logger.info("%s Intermediate output %s (%s) will be trashed%s%s%s." % (
390 self.arvrunner.label(self), record["output_uuid"], container["output"], aftertime, orpart, oncomplete))
391 self.arvrunner.add_intermediate_output(record["output_uuid"])
393 if container["output"]:
394 outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
395 except WorkflowException as e:
396 # Only include a stack trace if in debug mode.
397 # A stack trace may obfuscate more useful output about the workflow.
398 logger.error("%s unable to collect output from %s:\n%s",
399 self.arvrunner.label(self), container["output"], e, exc_info=(e if self.arvrunner.debug else False))
400 processStatus = "permanentFail"
402 logger.exception("%s while getting output object:", self.arvrunner.label(self))
403 processStatus = "permanentFail"
405 self.output_callback(outputs, processStatus)
408 class RunnerContainer(Runner):
409 """Submit and manage a container that runs arvados-cwl-runner."""
411 def arvados_job_spec(self, runtimeContext):
412 """Create an Arvados container request for this workflow.
414 The returned dict can be used to create a container passed as
415 the +body+ argument to container_requests().create().
418 adjustDirObjs(self.job_order, trim_listing)
419 visit_class(self.job_order, ("File", "Directory"), trim_anonymous_location)
420 visit_class(self.job_order, ("File", "Directory"), remove_redundant_fields)
423 for param in sorted(self.job_order.keys()):
424 if self.secret_store.has_secret(self.job_order[param]):
425 mnt = "/secrets/s%d" % len(secret_mounts)
426 secret_mounts[mnt] = {
428 "content": self.secret_store.retrieve(self.job_order[param])
430 self.job_order[param] = {"$include": mnt}
434 "output_path": "/var/spool/cwl",
435 "cwd": "/var/spool/cwl",
436 "priority": self.priority,
437 "state": "Committed",
438 "container_image": arvados_jobs_image(self.arvrunner, self.jobs_image),
440 "/var/lib/cwl/cwl.input.json": {
442 "content": self.job_order
446 "path": "/var/spool/cwl/cwl.output.json"
449 "kind": "collection",
453 "secret_mounts": secret_mounts,
454 "runtime_constraints": {
455 "vcpus": math.ceil(self.submit_runner_cores),
456 "ram": 1024*1024 * (math.ceil(self.submit_runner_ram) + math.ceil(self.collection_cache_size)),
459 "use_existing": False, # Never reuse the runner container - see #15497.
463 if self.embedded_tool.tool.get("id", "").startswith("keep:"):
464 sp = self.embedded_tool.tool["id"].split('/')
465 workflowcollection = sp[0][5:]
466 workflowname = "/".join(sp[1:])
467 workflowpath = "/var/lib/cwl/workflow/%s" % workflowname
468 container_req["mounts"]["/var/lib/cwl/workflow"] = {
469 "kind": "collection",
470 "portable_data_hash": "%s" % workflowcollection
473 packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map)
474 workflowpath = "/var/lib/cwl/workflow.json#main"
475 container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
479 if self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
480 container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
482 properties_req, _ = self.embedded_tool.get_requirement("http://arvados.org/cwl#ProcessProperties")
484 builder = make_builder(self.job_order, self.embedded_tool.hints, self.embedded_tool.requirements, runtimeContext, self.embedded_tool.metadata)
485 print("ZZZZZZ", properties_req["processProperties"])
486 for pr in properties_req["processProperties"]:
488 container_req["properties"][pr["propertyName"]] = builder.do_eval(pr["propertyValue"])
490 # --local means execute the workflow instead of submitting a container request
491 # --api=containers means use the containers API
492 # --no-log-timestamps means don't add timestamps (the logging infrastructure does this)
493 # --disable-validate because we already validated so don't need to do it again
494 # --eval-timeout is the timeout for javascript invocation
495 # --parallel-task-count is the number of threads to use for job submission
496 # --enable/disable-reuse sets desired job reuse
497 # --collection-cache-size sets aside memory to store collections
498 command = ["arvados-cwl-runner",
501 "--no-log-timestamps",
502 "--disable-validate",
504 "--eval-timeout=%s" % self.arvrunner.eval_timeout,
505 "--thread-count=%s" % self.arvrunner.thread_count,
506 "--enable-reuse" if self.enable_reuse else "--disable-reuse",
507 "--collection-cache-size=%s" % self.collection_cache_size]
510 command.append("--output-name=" + self.output_name)
511 container_req["output_name"] = self.output_name
514 command.append("--output-tags=" + self.output_tags)
516 if runtimeContext.debug:
517 command.append("--debug")
519 if runtimeContext.storage_classes != "default":
520 command.append("--storage-classes=" + runtimeContext.storage_classes)
522 if runtimeContext.intermediate_storage_classes != "default":
523 command.append("--intermediate-storage-classes=" + runtimeContext.intermediate_storage_classes)
526 command.append("--on-error=" + self.on_error)
528 if self.intermediate_output_ttl:
529 command.append("--intermediate-output-ttl=%d" % self.intermediate_output_ttl)
531 if self.arvrunner.trash_intermediate:
532 command.append("--trash-intermediate")
534 if self.arvrunner.project_uuid:
535 command.append("--project-uuid="+self.arvrunner.project_uuid)
538 command.append("--enable-dev")
540 command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
542 container_req["command"] = command
547 def run(self, runtimeContext):
548 runtimeContext.keepprefix = "keep:"
549 job_spec = self.arvados_job_spec(runtimeContext)
550 if self.arvrunner.project_uuid:
551 job_spec["owner_uuid"] = self.arvrunner.project_uuid
553 extra_submit_params = {}
554 if runtimeContext.submit_runner_cluster:
555 extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster
557 if runtimeContext.submit_request_uuid:
558 if "cluster_id" in extra_submit_params:
559 # Doesn't make sense for "update" and actually fails
560 del extra_submit_params["cluster_id"]
561 response = self.arvrunner.api.container_requests().update(
562 uuid=runtimeContext.submit_request_uuid,
564 **extra_submit_params
565 ).execute(num_retries=self.arvrunner.num_retries)
567 response = self.arvrunner.api.container_requests().create(
569 **extra_submit_params
570 ).execute(num_retries=self.arvrunner.num_retries)
572 self.uuid = response["uuid"]
573 self.arvrunner.process_submitted(self)
575 logger.info("%s submitted container_request %s", self.arvrunner.label(self), response["uuid"])
577 workbench1 = self.arvrunner.api.config()["Services"]["Workbench1"]["ExternalURL"]
578 workbench2 = self.arvrunner.api.config()["Services"]["Workbench2"]["ExternalURL"]
581 url = "{}processes/{}".format(workbench2, response["uuid"])
583 url = "{}container_requests/{}".format(workbench1, response["uuid"])
585 logger.info("Monitor workflow progress at %s", url)
588 def done(self, record):
590 container = self.arvrunner.api.containers().get(
591 uuid=record["container_uuid"]
592 ).execute(num_retries=self.arvrunner.num_retries)
593 container["log"] = record["log_uuid"]
595 logger.exception("%s while getting runner container", self.arvrunner.label(self))
596 self.arvrunner.output_callback({}, "permanentFail")
598 super(RunnerContainer, self).done(container)