1 # Copyright (C) The Arvados Authors. All rights reserved.
3 # SPDX-License-Identifier: Apache-2.0
11 from cwltool.process import shortname, UnsupportedRequirement
12 from cwltool.errors import WorkflowException
13 from cwltool.command_line_tool import revmap_file, CommandLineTool
14 from cwltool.load_tool import fetch_document
15 from cwltool.builder import Builder
16 from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
17 from cwltool.job import JobBase
19 from schema_salad.sourceline import SourceLine
21 import arvados_cwl.util
22 import ruamel.yaml as yaml
24 import arvados.collection
25 from arvados.errors import ApiError
27 from .arvdocker import arv_docker_get_image
28 from .runner import Runner, arvados_jobs_image, packed_workflow, upload_workflow_collection, trim_anonymous_location, remove_redundant_fields
29 from .pathmapper import VwdPathMapper, trim_listing
30 from .perf import Perf
32 from ._version import __version__
33 from .util import get_intermediate_collection_info
35 logger = logging.getLogger('arvados.cwl-runner')
36 metrics = logging.getLogger('arvados.cwl-runner.metrics')
38 crunchrunner_re = re.compile(r"^.*crunchrunner: \$\(task\.(tmpdir|outdir|keep)\)=(.*)$")
40 crunchrunner_git_commit = 'a3f2cb186e437bfce0031b024b2157b73ed2717d'
42 class ArvadosJob(JobBase):
43 """Submit and manage a Crunch job for executing a CWL CommandLineTool."""
45 def __init__(self, runner,
46 builder, # type: Builder
47 joborder, # type: Dict[Text, Union[Dict[Text, Any], List, Text]]
48 make_path_mapper, # type: Callable[..., PathMapper]
49 requirements, # type: List[Dict[Text, Text]]
50 hints, # type: List[Dict[Text, Text]]
53 super(ArvadosJob, self).__init__(builder, joborder, make_path_mapper, requirements, hints, name)
54 self.arvrunner = runner
58 def run(self, runtimeContext):
60 "command": self.command_line
62 runtime_constraints = {}
64 with Perf(metrics, "generatefiles %s" % self.name):
65 if self.generatefiles["listing"]:
66 vwd = arvados.collection.Collection(api_client=self.arvrunner.api,
67 keep_client=self.arvrunner.keep_client,
68 num_retries=self.arvrunner.num_retries)
69 script_parameters["task.vwd"] = {}
70 generatemapper = VwdPathMapper(self.generatefiles["listing"], "", "",
73 with Perf(metrics, "createfiles %s" % self.name):
74 for f, p in generatemapper.items():
75 if p.type == "CreateFile":
76 with vwd.open(p.target, "w") as n:
77 n.write(p.resolved.encode("utf-8"))
80 with Perf(metrics, "generatefiles.save_new %s" % self.name):
81 info = get_intermediate_collection_info(self.name, None, runtimeContext.intermediate_output_ttl)
82 vwd.save_new(name=info["name"],
83 owner_uuid=self.arvrunner.project_uuid,
84 ensure_unique_name=True,
85 trash_at=info["trash_at"],
86 properties=info["properties"])
88 for f, p in generatemapper.items():
90 script_parameters["task.vwd"][p.target] = p.resolved
91 if p.type == "CreateFile":
92 script_parameters["task.vwd"][p.target] = "$(task.keep)/%s/%s" % (vwd.portable_data_hash(), p.target)
94 script_parameters["task.env"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
96 script_parameters["task.env"].update(self.environment)
99 script_parameters["task.stdin"] = self.stdin
102 script_parameters["task.stdout"] = self.stdout
105 script_parameters["task.stderr"] = self.stderr
107 if self.successCodes:
108 script_parameters["task.successCodes"] = self.successCodes
109 if self.temporaryFailCodes:
110 script_parameters["task.temporaryFailCodes"] = self.temporaryFailCodes
111 if self.permanentFailCodes:
112 script_parameters["task.permanentFailCodes"] = self.permanentFailCodes
114 with Perf(metrics, "arv_docker_get_image %s" % self.name):
115 (docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
116 if docker_req and runtimeContext.use_container is not False:
117 if docker_req.get("dockerOutputDirectory"):
118 raise SourceLine(docker_req, "dockerOutputDirectory", UnsupportedRequirement).makeError(
119 "Option 'dockerOutputDirectory' of DockerRequirement not supported.")
120 runtime_constraints["docker_image"] = arv_docker_get_image(self.arvrunner.api,
122 runtimeContext.pull_image,
123 self.arvrunner.project_uuid)
125 runtime_constraints["docker_image"] = "arvados/jobs"
127 resources = self.builder.resources
128 if resources is not None:
129 runtime_constraints["min_cores_per_node"] = resources.get("cores", 1)
130 runtime_constraints["min_ram_mb_per_node"] = resources.get("ram")
131 runtime_constraints["min_scratch_mb_per_node"] = resources.get("tmpdirSize", 0) + resources.get("outdirSize", 0)
133 runtime_req, _ = self.get_requirement("http://arvados.org/cwl#RuntimeConstraints")
135 if "keep_cache" in runtime_req:
136 runtime_constraints["keep_cache_mb_per_task"] = runtime_req["keep_cache"]
137 runtime_constraints["min_ram_mb_per_node"] += runtime_req["keep_cache"]
138 if "outputDirType" in runtime_req:
139 if runtime_req["outputDirType"] == "local_output_dir":
140 script_parameters["task.keepTmpOutput"] = False
141 elif runtime_req["outputDirType"] == "keep_output_dir":
142 script_parameters["task.keepTmpOutput"] = True
144 filters = [["repository", "=", "arvados"],
145 ["script", "=", "crunchrunner"],
146 ["script_version", "in git", crunchrunner_git_commit]]
147 if not self.arvrunner.ignore_docker_for_reuse:
148 filters.append(["docker_image_locator", "in docker", runtime_constraints["docker_image"]])
150 enable_reuse = runtimeContext.enable_reuse
152 reuse_req, _ = self.get_requirement("http://arvados.org/cwl#ReuseRequirement")
154 enable_reuse = reuse_req["enableReuse"]
156 self.output_callback = self.arvrunner.get_wrapped_callback(self.output_callback)
159 with Perf(metrics, "create %s" % self.name):
160 response = self.arvrunner.api.jobs().create(
162 "owner_uuid": self.arvrunner.project_uuid,
163 "script": "crunchrunner",
164 "repository": "arvados",
165 "script_version": "master",
166 "minimum_script_version": crunchrunner_git_commit,
167 "script_parameters": {"tasks": [script_parameters]},
168 "runtime_constraints": runtime_constraints
171 find_or_create=enable_reuse
172 ).execute(num_retries=self.arvrunner.num_retries)
174 self.uuid = response["uuid"]
175 self.arvrunner.process_submitted(self)
177 self.update_pipeline_component(response)
179 if response["state"] == "Complete":
180 logger.info("%s reused job %s", self.arvrunner.label(self), response["uuid"])
181 # Give read permission to the desired project on reused jobs
182 if response["owner_uuid"] != self.arvrunner.project_uuid:
184 self.arvrunner.api.links().create(body={
185 'link_class': 'permission',
187 'tail_uuid': self.arvrunner.project_uuid,
188 'head_uuid': response["uuid"],
189 }).execute(num_retries=self.arvrunner.num_retries)
190 except ApiError as e:
191 # The user might not have "manage" access on the job: log
192 # a message and continue.
193 logger.info("Creating read permission on job %s: %s",
197 logger.info("%s %s is %s", self.arvrunner.label(self), response["uuid"], response["state"])
198 except Exception as e:
199 logger.exception("%s error" % (self.arvrunner.label(self)))
200 self.output_callback({}, "permanentFail")
202 def update_pipeline_component(self, record):
203 with self.arvrunner.workflow_eval_lock:
204 if self.arvrunner.pipeline:
205 self.arvrunner.pipeline["components"][self.name] = {"job": record}
206 with Perf(metrics, "update_pipeline_component %s" % self.name):
207 self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().update(
208 uuid=self.arvrunner.pipeline["uuid"],
210 "components": self.arvrunner.pipeline["components"]
211 }).execute(num_retries=self.arvrunner.num_retries)
212 if self.arvrunner.uuid:
214 job = self.arvrunner.api.jobs().get(uuid=self.arvrunner.uuid).execute()
216 components = job["components"]
217 components[self.name] = record["uuid"]
218 self.arvrunner.api.jobs().update(
219 uuid=self.arvrunner.uuid,
221 "components": components
222 }).execute(num_retries=self.arvrunner.num_retries)
223 except Exception as e:
224 logger.info("Error adding to components: %s", e)
226 def done(self, record):
228 self.update_pipeline_component(record)
233 if record["state"] == "Complete":
234 processStatus = "success"
236 processStatus = "permanentFail"
241 with Perf(metrics, "inspect log %s" % self.name):
242 logc = arvados.collection.CollectionReader(record["log"],
243 api_client=self.arvrunner.api,
244 keep_client=self.arvrunner.keep_client,
245 num_retries=self.arvrunner.num_retries)
246 log = logc.open(logc.keys()[0])
253 # Determine the tmpdir, outdir and keep paths from
254 # the job run. Unfortunately, we can't take the first
255 # values we find (which are expected to be near the
256 # top) and stop scanning because if the node fails and
257 # the job restarts on a different node these values
258 # will different runs, and we need to know about the
259 # final run that actually produced output.
260 g = crunchrunner_re.match(l)
262 dirs[g.group(1)] = g.group(2)
264 if processStatus == "permanentFail":
265 done.logtail(logc, logger.error, "%s (%s) error log:" % (self.arvrunner.label(self), record["uuid"]), maxlen=40)
267 with Perf(metrics, "output collection %s" % self.name):
268 outputs = done.done(self, record, dirs["tmpdir"],
269 dirs["outdir"], dirs["keep"])
270 except WorkflowException as e:
271 logger.error("%s unable to collect output from %s:\n%s",
272 self.arvrunner.label(self), record["output"], e, exc_info=(e if self.arvrunner.debug else False))
273 processStatus = "permanentFail"
274 except Exception as e:
275 logger.exception("Got unknown exception while collecting output for job %s:", self.name)
276 processStatus = "permanentFail"
278 # Note: Currently, on error output_callback is expecting an empty dict,
279 # anything else will fail.
280 if not isinstance(outputs, dict):
281 logger.error("Unexpected output type %s '%s'", type(outputs), outputs)
283 processStatus = "permanentFail"
285 self.output_callback(outputs, processStatus)
288 class RunnerJob(Runner):
289 """Submit and manage a Crunch job that runs crunch_scripts/cwl-runner."""
291 def arvados_job_spec(self, debug=False):
292 """Create an Arvados job specification for this workflow.
294 The returned dict can be used to create a job (i.e., passed as
295 the +body+ argument to jobs().create()), or as a component in
296 a pipeline template or pipeline instance.
299 if self.embedded_tool.tool["id"].startswith("keep:"):
300 self.job_order["cwl:tool"] = self.embedded_tool.tool["id"][5:]
302 packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map)
303 wf_pdh = upload_workflow_collection(self.arvrunner, self.name, packed)
304 self.job_order["cwl:tool"] = "%s/workflow.cwl#main" % wf_pdh
306 adjustDirObjs(self.job_order, trim_listing)
307 visit_class(self.job_order, ("File", "Directory"), trim_anonymous_location)
308 visit_class(self.job_order, ("File", "Directory"), remove_redundant_fields)
311 self.job_order["arv:output_name"] = self.output_name
314 self.job_order["arv:output_tags"] = self.output_tags
316 self.job_order["arv:enable_reuse"] = self.enable_reuse
319 self.job_order["arv:on_error"] = self.on_error
322 self.job_order["arv:debug"] = True
325 "script": "cwl-runner",
326 "script_version": "master",
327 "minimum_script_version": "570509ab4d2ef93d870fd2b1f2eab178afb1bad9",
328 "repository": "arvados",
329 "script_parameters": self.job_order,
330 "runtime_constraints": {
331 "docker_image": arvados_jobs_image(self.arvrunner, self.jobs_image),
332 "min_ram_mb_per_node": self.submit_runner_ram
336 def run(self, runtimeContext):
337 job_spec = self.arvados_job_spec(runtimeContext.debug)
339 job_spec.setdefault("owner_uuid", self.arvrunner.project_uuid)
341 job = self.arvrunner.api.jobs().create(
343 find_or_create=self.enable_reuse
344 ).execute(num_retries=self.arvrunner.num_retries)
346 for k,v in job_spec["script_parameters"].items():
347 if v is False or v is None or isinstance(v, dict):
348 job_spec["script_parameters"][k] = {"value": v}
350 del job_spec["owner_uuid"]
351 job_spec["job"] = job
354 "owner_uuid": self.arvrunner.project_uuid,
357 "cwl-runner": job_spec,
359 "state": "RunningOnServer",
361 if not self.enable_reuse:
362 instance_spec["properties"] = {"run_options": {"enable_job_reuse": False}}
364 self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().create(
365 body=instance_spec).execute(num_retries=self.arvrunner.num_retries)
366 logger.info("Created pipeline %s", self.arvrunner.pipeline["uuid"])
368 if runtimeContext.wait is False:
369 self.uuid = self.arvrunner.pipeline["uuid"]
372 self.uuid = job["uuid"]
373 self.arvrunner.process_submitted(self)
376 class RunnerTemplate(object):
377 """An Arvados pipeline template that invokes a CWL workflow."""
379 type_to_dataclass = {
380 'boolean': 'boolean',
382 'Directory': 'Collection',
388 def __init__(self, runner, tool, job_order, enable_reuse, uuid,
389 submit_runner_ram=0, name=None, merged_map=None,
390 loadingContext=None):
392 self.embedded_tool = tool
393 self.job = RunnerJob(
396 enable_reuse=enable_reuse,
399 submit_runner_ram=submit_runner_ram,
401 merged_map=merged_map,
402 loadingContext=loadingContext)
403 self.job.job_order = job_order
406 def pipeline_component_spec(self):
407 """Return a component that Workbench and a-r-p-i will understand.
409 Specifically, translate CWL input specs to Arvados pipeline
410 format, like {"dataclass":"File","value":"xyz"}.
413 spec = self.job.arvados_job_spec()
415 # Most of the component spec is exactly the same as the job
416 # spec (script, script_version, etc.).
417 # spec['script_parameters'] isn't right, though. A component
418 # spec's script_parameters hash is a translation of
419 # self.tool.tool['inputs'] with defaults/overrides taken from
420 # the job order. So we move the job parameters out of the way
421 # and build a new spec['script_parameters'].
422 job_params = spec['script_parameters']
423 spec['script_parameters'] = {}
425 for param in self.embedded_tool.tool['inputs']:
426 param = copy.deepcopy(param)
428 # Data type and "required" flag...
429 types = param['type']
430 if not isinstance(types, list):
432 param['required'] = 'null' not in types
433 non_null_types = [t for t in types if t != "null"]
434 if len(non_null_types) == 1:
435 the_type = [c for c in non_null_types][0]
437 if isinstance(the_type, basestring):
438 dataclass = self.type_to_dataclass.get(the_type)
440 param['dataclass'] = dataclass
441 # Note: If we didn't figure out a single appropriate
442 # dataclass, we just left that attribute out. We leave
443 # the "type" attribute there in any case, which might help
446 # Title and description...
447 title = param.pop('label', '')
448 descr = param.pop('doc', '').rstrip('\n')
450 param['title'] = title
452 param['description'] = descr
454 # Fill in the value from the current job order, if any.
455 param_id = shortname(param.pop('id'))
456 value = job_params.get(param_id)
459 elif not isinstance(value, dict):
460 param['value'] = value
461 elif param.get('dataclass') in ('File', 'Collection') and value.get('location'):
462 param['value'] = value['location'][5:]
464 spec['script_parameters'][param_id] = param
465 spec['script_parameters']['cwl:tool'] = job_params['cwl:tool']
471 self.job.name: self.pipeline_component_spec(),
473 "name": self.job.name,
475 if self.runner.project_uuid:
476 body["owner_uuid"] = self.runner.project_uuid
478 self.runner.api.pipeline_templates().update(
479 uuid=self.uuid, body=body).execute(
480 num_retries=self.runner.num_retries)
481 logger.info("Updated template %s", self.uuid)
483 self.uuid = self.runner.api.pipeline_templates().create(
484 body=body, ensure_unique_name=True).execute(
485 num_retries=self.runner.num_retries)['uuid']
486 logger.info("Created template %s", self.uuid)