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.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
25 from cwltool.utils import aslist
26 from cwltool.job import JobBase
28 import arvados.collection
30 from .arvdocker import arv_docker_get_image
32 from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location, remove_redundant_fields
33 from .fsaccess import CollectionFetcher
34 from .pathmapper import NoFollowPathMapper, trim_listing
35 from .perf import Perf
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
71 "command": self.command_line,
73 "output_path": self.outdir,
75 "priority": runtimeContext.priority,
79 runtime_constraints = {}
81 if runtimeContext.project_uuid:
82 container_request["owner_uuid"] = runtimeContext.project_uuid
84 if self.arvrunner.secret_store.has_secret(self.command_line):
85 raise WorkflowException("Secret material leaked on command line, only file literals may contain secrets")
87 if self.arvrunner.secret_store.has_secret(self.environment):
88 raise WorkflowException("Secret material leaked in environment, only file literals may contain secrets")
90 resources = self.builder.resources
91 if resources is not None:
92 runtime_constraints["vcpus"] = math.ceil(resources.get("cores", 1))
93 runtime_constraints["ram"] = math.ceil(resources.get("ram") * 2**20)
98 "capacity": math.ceil(resources.get("outdirSize", 0) * 2**20)
102 "capacity": math.ceil(resources.get("tmpdirSize", 0) * 2**20)
106 scheduling_parameters = {}
108 rf = [self.pathmapper.mapper(f) for f in self.pathmapper.referenced_files]
109 rf.sort(key=lambda k: k.resolved)
111 for resolved, target, tp, stg in rf:
114 if prevdir and target.startswith(prevdir):
116 if tp == "Directory":
119 targetdir = os.path.dirname(target)
120 sp = resolved.split("/", 1)
121 pdh = sp[0][5:] # remove "keep:"
122 mounts[targetdir] = {
123 "kind": "collection",
124 "portable_data_hash": pdh
126 if pdh in self.pathmapper.pdh_to_uuid:
127 mounts[targetdir]["uuid"] = self.pathmapper.pdh_to_uuid[pdh]
129 if tp == "Directory":
132 path = os.path.dirname(sp[1])
133 if path and path != "/":
134 mounts[targetdir]["path"] = path
135 prevdir = targetdir + "/"
137 with Perf(metrics, "generatefiles %s" % self.name):
138 if self.generatefiles["listing"]:
139 vwd = arvados.collection.Collection(api_client=self.arvrunner.api,
140 keep_client=self.arvrunner.keep_client,
141 num_retries=self.arvrunner.num_retries)
142 generatemapper = NoFollowPathMapper(self.generatefiles["listing"], "", "",
145 sorteditems = sorted(generatemapper.items(), key=lambda n: n[1].target)
147 logger.debug("generatemapper is %s", sorteditems)
149 with Perf(metrics, "createfiles %s" % self.name):
150 for f, p in sorteditems:
153 elif p.type in ("File", "Directory", "WritableFile", "WritableDirectory"):
154 if p.resolved.startswith("_:"):
157 source, path = self.arvrunner.fs_access.get_collection(p.resolved)
158 vwd.copy(path, p.target, source_collection=source)
159 elif p.type == "CreateFile":
160 if self.arvrunner.secret_store.has_secret(p.resolved):
161 secret_mounts["%s/%s" % (self.outdir, p.target)] = {
163 "content": self.arvrunner.secret_store.retrieve(p.resolved)
166 with vwd.open(p.target, "w") as n:
169 def keepemptydirs(p):
170 if isinstance(p, arvados.collection.RichCollectionBase):
172 p.open(".keep", "w").close()
179 if not runtimeContext.current_container:
180 runtimeContext.current_container = arvados_cwl.util.get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger)
181 info = arvados_cwl.util.get_intermediate_collection_info(self.name, runtimeContext.current_container, runtimeContext.intermediate_output_ttl)
182 vwd.save_new(name=info["name"],
183 owner_uuid=runtimeContext.project_uuid,
184 ensure_unique_name=True,
185 trash_at=info["trash_at"],
186 properties=info["properties"])
189 for f, p in sorteditems:
190 if (not p.target or self.arvrunner.secret_store.has_secret(p.resolved) or
191 (prev is not None and p.target.startswith(prev))):
193 mountpoint = "%s/%s" % (self.outdir, p.target)
194 mounts[mountpoint] = {"kind": "collection",
195 "portable_data_hash": vwd.portable_data_hash(),
197 if p.type.startswith("Writable"):
198 mounts[mountpoint]["writable"] = True
199 prev = p.target + "/"
201 container_request["environment"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
203 container_request["environment"].update(self.environment)
206 sp = self.stdin[6:].split("/", 1)
207 mounts["stdin"] = {"kind": "collection",
208 "portable_data_hash": sp[0],
212 mounts["stderr"] = {"kind": "file",
213 "path": "%s/%s" % (self.outdir, self.stderr)}
216 mounts["stdout"] = {"kind": "file",
217 "path": "%s/%s" % (self.outdir, self.stdout)}
219 (docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
221 docker_req = {"dockerImageId": "arvados/jobs"}
223 container_request["container_image"] = arv_docker_get_image(self.arvrunner.api,
225 runtimeContext.pull_image,
226 runtimeContext.project_uuid)
228 api_req, _ = self.get_requirement("http://arvados.org/cwl#APIRequirement")
230 runtime_constraints["API"] = True
232 runtime_req, _ = self.get_requirement("http://arvados.org/cwl#RuntimeConstraints")
234 if "keep_cache" in runtime_req:
235 runtime_constraints["keep_cache_ram"] = math.ceil(runtime_req["keep_cache"] * 2**20)
236 if "outputDirType" in runtime_req:
237 if runtime_req["outputDirType"] == "local_output_dir":
238 # Currently the default behavior.
240 elif runtime_req["outputDirType"] == "keep_output_dir":
241 mounts[self.outdir]= {
242 "kind": "collection",
246 partition_req, _ = self.get_requirement("http://arvados.org/cwl#PartitionRequirement")
248 scheduling_parameters["partitions"] = aslist(partition_req["partition"])
250 intermediate_output_req, _ = self.get_requirement("http://arvados.org/cwl#IntermediateOutput")
251 if intermediate_output_req:
252 self.output_ttl = intermediate_output_req["outputTTL"]
254 self.output_ttl = self.arvrunner.intermediate_output_ttl
256 if self.output_ttl < 0:
257 raise WorkflowException("Invalid value %d for output_ttl, cannot be less than zero" % container_request["output_ttl"])
259 if self.timelimit is not None:
260 scheduling_parameters["max_run_time"] = self.timelimit
262 extra_submit_params = {}
263 if runtimeContext.submit_runner_cluster:
264 extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster
266 container_request["output_name"] = "Output for step %s" % (self.name)
267 container_request["output_ttl"] = self.output_ttl
268 container_request["mounts"] = mounts
269 container_request["secret_mounts"] = secret_mounts
270 container_request["runtime_constraints"] = runtime_constraints
271 container_request["scheduling_parameters"] = scheduling_parameters
273 enable_reuse = runtimeContext.enable_reuse
275 reuse_req, _ = self.get_requirement("http://arvados.org/cwl#ReuseRequirement")
277 enable_reuse = reuse_req["enableReuse"]
278 container_request["use_existing"] = enable_reuse
280 if runtimeContext.runnerjob.startswith("arvwf:"):
281 wfuuid = runtimeContext.runnerjob[6:runtimeContext.runnerjob.index("#")]
282 wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(num_retries=self.arvrunner.num_retries)
283 if container_request["name"] == "main":
284 container_request["name"] = wfrecord["name"]
285 container_request["properties"]["template_uuid"] = wfuuid
287 self.output_callback = self.arvrunner.get_wrapped_callback(self.output_callback)
290 if runtimeContext.submit_request_uuid:
291 response = self.arvrunner.api.container_requests().update(
292 uuid=runtimeContext.submit_request_uuid,
293 body=container_request,
294 **extra_submit_params
295 ).execute(num_retries=self.arvrunner.num_retries)
297 response = self.arvrunner.api.container_requests().create(
298 body=container_request,
299 **extra_submit_params
300 ).execute(num_retries=self.arvrunner.num_retries)
302 self.uuid = response["uuid"]
303 self.arvrunner.process_submitted(self)
305 if response["state"] == "Final":
306 logger.info("%s reused container %s", self.arvrunner.label(self), response["container_uuid"])
308 logger.info("%s %s state is %s", self.arvrunner.label(self), response["uuid"], response["state"])
310 logger.exception("%s got an error", self.arvrunner.label(self))
311 self.output_callback({}, "permanentFail")
313 def done(self, record):
316 container = self.arvrunner.api.containers().get(
317 uuid=record["container_uuid"]
318 ).execute(num_retries=self.arvrunner.num_retries)
319 if container["state"] == "Complete":
320 rcode = container["exit_code"]
321 if self.successCodes and rcode in self.successCodes:
322 processStatus = "success"
323 elif self.temporaryFailCodes and rcode in self.temporaryFailCodes:
324 processStatus = "temporaryFail"
325 elif self.permanentFailCodes and rcode in self.permanentFailCodes:
326 processStatus = "permanentFail"
328 processStatus = "success"
330 processStatus = "permanentFail"
332 processStatus = "permanentFail"
334 if processStatus == "permanentFail" and record["log_uuid"]:
335 logc = arvados.collection.CollectionReader(record["log_uuid"],
336 api_client=self.arvrunner.api,
337 keep_client=self.arvrunner.keep_client,
338 num_retries=self.arvrunner.num_retries)
339 label = self.arvrunner.label(self)
342 "%s (%s) error log:" % (label, record["uuid"]), maxlen=40)
344 if record["output_uuid"]:
345 if self.arvrunner.trash_intermediate or self.arvrunner.intermediate_output_ttl:
346 # Compute the trash time to avoid requesting the collection record.
347 trash_at = ciso8601.parse_datetime_as_naive(record["modified_at"]) + datetime.timedelta(0, self.arvrunner.intermediate_output_ttl)
348 aftertime = " at %s" % trash_at.strftime("%Y-%m-%d %H:%M:%S UTC") if self.arvrunner.intermediate_output_ttl else ""
349 orpart = ", or" if self.arvrunner.trash_intermediate and self.arvrunner.intermediate_output_ttl else ""
350 oncomplete = " upon successful completion of the workflow" if self.arvrunner.trash_intermediate else ""
351 logger.info("%s Intermediate output %s (%s) will be trashed%s%s%s." % (
352 self.arvrunner.label(self), record["output_uuid"], container["output"], aftertime, orpart, oncomplete))
353 self.arvrunner.add_intermediate_output(record["output_uuid"])
355 if container["output"]:
356 outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
357 except WorkflowException as e:
358 # Only include a stack trace if in debug mode.
359 # A stack trace may obfuscate more useful output about the workflow.
360 logger.error("%s unable to collect output from %s:\n%s",
361 self.arvrunner.label(self), container["output"], e, exc_info=(e if self.arvrunner.debug else False))
362 processStatus = "permanentFail"
364 logger.exception("%s while getting output object:", self.arvrunner.label(self))
365 processStatus = "permanentFail"
367 self.output_callback(outputs, processStatus)
370 class RunnerContainer(Runner):
371 """Submit and manage a container that runs arvados-cwl-runner."""
373 def arvados_job_spec(self, runtimeContext):
374 """Create an Arvados container request for this workflow.
376 The returned dict can be used to create a container passed as
377 the +body+ argument to container_requests().create().
380 adjustDirObjs(self.job_order, trim_listing)
381 visit_class(self.job_order, ("File", "Directory"), trim_anonymous_location)
382 visit_class(self.job_order, ("File", "Directory"), remove_redundant_fields)
385 for param in sorted(self.job_order.keys()):
386 if self.secret_store.has_secret(self.job_order[param]):
387 mnt = "/secrets/s%d" % len(secret_mounts)
388 secret_mounts[mnt] = {
390 "content": self.secret_store.retrieve(self.job_order[param])
392 self.job_order[param] = {"$include": mnt}
396 "output_path": "/var/spool/cwl",
397 "cwd": "/var/spool/cwl",
398 "priority": self.priority,
399 "state": "Committed",
400 "container_image": arvados_jobs_image(self.arvrunner, self.jobs_image),
402 "/var/lib/cwl/cwl.input.json": {
404 "content": self.job_order
408 "path": "/var/spool/cwl/cwl.output.json"
411 "kind": "collection",
415 "secret_mounts": secret_mounts,
416 "runtime_constraints": {
417 "vcpus": math.ceil(self.submit_runner_cores),
418 "ram": 1024*1024 * (math.ceil(self.submit_runner_ram) + math.ceil(self.collection_cache_size)),
421 "use_existing": self.enable_reuse,
425 if self.embedded_tool.tool.get("id", "").startswith("keep:"):
426 sp = self.embedded_tool.tool["id"].split('/')
427 workflowcollection = sp[0][5:]
428 workflowname = "/".join(sp[1:])
429 workflowpath = "/var/lib/cwl/workflow/%s" % workflowname
430 container_req["mounts"]["/var/lib/cwl/workflow"] = {
431 "kind": "collection",
432 "portable_data_hash": "%s" % workflowcollection
435 packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map)
436 workflowpath = "/var/lib/cwl/workflow.json#main"
437 container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
441 if self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
442 container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
445 # --local means execute the workflow instead of submitting a container request
446 # --api=containers means use the containers API
447 # --no-log-timestamps means don't add timestamps (the logging infrastructure does this)
448 # --disable-validate because we already validated so don't need to do it again
449 # --eval-timeout is the timeout for javascript invocation
450 # --parallel-task-count is the number of threads to use for job submission
451 # --enable/disable-reuse sets desired job reuse
452 # --collection-cache-size sets aside memory to store collections
453 command = ["arvados-cwl-runner",
456 "--no-log-timestamps",
457 "--disable-validate",
458 "--eval-timeout=%s" % self.arvrunner.eval_timeout,
459 "--thread-count=%s" % self.arvrunner.thread_count,
460 "--enable-reuse" if self.enable_reuse else "--disable-reuse",
461 "--collection-cache-size=%s" % self.collection_cache_size]
464 command.append("--output-name=" + self.output_name)
465 container_req["output_name"] = self.output_name
468 command.append("--output-tags=" + self.output_tags)
470 if runtimeContext.debug:
471 command.append("--debug")
473 if runtimeContext.storage_classes != "default":
474 command.append("--storage-classes=" + runtimeContext.storage_classes)
477 command.append("--on-error=" + self.on_error)
479 if self.intermediate_output_ttl:
480 command.append("--intermediate-output-ttl=%d" % self.intermediate_output_ttl)
482 if self.arvrunner.trash_intermediate:
483 command.append("--trash-intermediate")
485 if self.arvrunner.project_uuid:
486 command.append("--project-uuid="+self.arvrunner.project_uuid)
488 command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
490 container_req["command"] = command
495 def run(self, runtimeContext):
496 runtimeContext.keepprefix = "keep:"
497 job_spec = self.arvados_job_spec(runtimeContext)
498 if self.arvrunner.project_uuid:
499 job_spec["owner_uuid"] = self.arvrunner.project_uuid
501 extra_submit_params = {}
502 if runtimeContext.submit_runner_cluster:
503 extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster
505 if runtimeContext.submit_request_uuid:
506 if "cluster_id" in extra_submit_params:
507 # Doesn't make sense for "update" and actually fails
508 del extra_submit_params["cluster_id"]
509 response = self.arvrunner.api.container_requests().update(
510 uuid=runtimeContext.submit_request_uuid,
512 **extra_submit_params
513 ).execute(num_retries=self.arvrunner.num_retries)
515 response = self.arvrunner.api.container_requests().create(
517 **extra_submit_params
518 ).execute(num_retries=self.arvrunner.num_retries)
520 self.uuid = response["uuid"]
521 self.arvrunner.process_submitted(self)
523 logger.info("%s submitted container_request %s", self.arvrunner.label(self), response["uuid"])
525 def done(self, record):
527 container = self.arvrunner.api.containers().get(
528 uuid=record["container_uuid"]
529 ).execute(num_retries=self.arvrunner.num_retries)
531 logger.exception("%s while getting runner container", self.arvrunner.label(self))
532 self.arvrunner.output_callback({}, "permanentFail")
534 super(RunnerContainer, self).done(container)