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 from arvados_cwl.util import get_current_container, get_intermediate_collection_info
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__
34 logger = logging.getLogger('arvados.cwl-runner')
35 metrics = logging.getLogger('arvados.cwl-runner.metrics')
37 crunchrunner_re = re.compile(r"^.*crunchrunner: \$\(task\.(tmpdir|outdir|keep)\)=(.*)$")
39 crunchrunner_git_commit = 'a3f2cb186e437bfce0031b024b2157b73ed2717d'
41 class ArvadosJob(JobBase):
42 """Submit and manage a Crunch job for executing a CWL CommandLineTool."""
44 def __init__(self, runner,
45 builder, # type: Builder
46 joborder, # type: Dict[Text, Union[Dict[Text, Any], List, Text]]
47 make_path_mapper, # type: Callable[..., PathMapper]
48 requirements, # type: List[Dict[Text, Text]]
49 hints, # type: List[Dict[Text, Text]]
52 super(ArvadosJob, self).__init__(builder, joborder, make_path_mapper, requirements, hints, name)
53 self.arvrunner = runner
57 def run(self, runtimeContext):
59 "command": self.command_line
61 runtime_constraints = {}
63 with Perf(metrics, "generatefiles %s" % self.name):
64 if self.generatefiles["listing"]:
65 vwd = arvados.collection.Collection(api_client=self.arvrunner.api,
66 keep_client=self.arvrunner.keep_client,
67 num_retries=self.arvrunner.num_retries)
68 script_parameters["task.vwd"] = {}
69 generatemapper = VwdPathMapper([self.generatefiles], "", "",
72 with Perf(metrics, "createfiles %s" % self.name):
73 for f, p in generatemapper.items():
74 if p.type == "CreateFile":
75 with vwd.open(p.target, "w") as n:
76 n.write(p.resolved.encode("utf-8"))
79 with Perf(metrics, "generatefiles.save_new %s" % self.name):
80 if not runtimeContext.current_container:
81 runtimeContext.current_container = get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger)
82 info = get_intermediate_collection_info(self.name, runtimeContext.current_container, runtimeContext.intermediate_output_ttl)
83 vwd.save_new(name=info["name"],
84 owner_uuid=self.arvrunner.project_uuid,
85 ensure_unique_name=True,
86 trash_at=info["trash_at"],
87 properties=info["properties"])
89 for f, p in generatemapper.items():
91 script_parameters["task.vwd"][p.target] = p.resolved
92 if p.type == "CreateFile":
93 script_parameters["task.vwd"][p.target] = "$(task.keep)/%s/%s" % (vwd.portable_data_hash(), p.target)
95 script_parameters["task.env"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
97 script_parameters["task.env"].update(self.environment)
100 script_parameters["task.stdin"] = self.stdin
103 script_parameters["task.stdout"] = self.stdout
106 script_parameters["task.stderr"] = self.stderr
108 if self.successCodes:
109 script_parameters["task.successCodes"] = self.successCodes
110 if self.temporaryFailCodes:
111 script_parameters["task.temporaryFailCodes"] = self.temporaryFailCodes
112 if self.permanentFailCodes:
113 script_parameters["task.permanentFailCodes"] = self.permanentFailCodes
115 with Perf(metrics, "arv_docker_get_image %s" % self.name):
116 (docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
117 if docker_req and runtimeContext.use_container is not False:
118 if docker_req.get("dockerOutputDirectory"):
119 raise SourceLine(docker_req, "dockerOutputDirectory", UnsupportedRequirement).makeError(
120 "Option 'dockerOutputDirectory' of DockerRequirement not supported.")
121 runtime_constraints["docker_image"] = arv_docker_get_image(self.arvrunner.api,
123 runtimeContext.pull_image,
124 self.arvrunner.project_uuid)
126 runtime_constraints["docker_image"] = "arvados/jobs"
128 resources = self.builder.resources
129 if resources is not None:
130 runtime_constraints["min_cores_per_node"] = resources.get("cores", 1)
131 runtime_constraints["min_ram_mb_per_node"] = resources.get("ram")
132 runtime_constraints["min_scratch_mb_per_node"] = resources.get("tmpdirSize", 0) + resources.get("outdirSize", 0)
134 runtime_req, _ = self.get_requirement("http://arvados.org/cwl#RuntimeConstraints")
136 if "keep_cache" in runtime_req:
137 runtime_constraints["keep_cache_mb_per_task"] = runtime_req["keep_cache"]
138 runtime_constraints["min_ram_mb_per_node"] += runtime_req["keep_cache"]
139 if "outputDirType" in runtime_req:
140 if runtime_req["outputDirType"] == "local_output_dir":
141 script_parameters["task.keepTmpOutput"] = False
142 elif runtime_req["outputDirType"] == "keep_output_dir":
143 script_parameters["task.keepTmpOutput"] = True
145 filters = [["repository", "=", "arvados"],
146 ["script", "=", "crunchrunner"],
147 ["script_version", "in git", crunchrunner_git_commit]]
148 if not self.arvrunner.ignore_docker_for_reuse:
149 filters.append(["docker_image_locator", "in docker", runtime_constraints["docker_image"]])
151 enable_reuse = runtimeContext.enable_reuse
153 reuse_req, _ = self.get_requirement("http://arvados.org/cwl#ReuseRequirement")
155 enable_reuse = reuse_req["enableReuse"]
157 self.output_callback = self.arvrunner.get_wrapped_callback(self.output_callback)
160 with Perf(metrics, "create %s" % self.name):
161 response = self.arvrunner.api.jobs().create(
163 "owner_uuid": self.arvrunner.project_uuid,
164 "script": "crunchrunner",
165 "repository": "arvados",
166 "script_version": "master",
167 "minimum_script_version": crunchrunner_git_commit,
168 "script_parameters": {"tasks": [script_parameters]},
169 "runtime_constraints": runtime_constraints
172 find_or_create=enable_reuse
173 ).execute(num_retries=self.arvrunner.num_retries)
175 self.uuid = response["uuid"]
176 self.arvrunner.process_submitted(self)
178 self.update_pipeline_component(response)
180 if response["state"] == "Complete":
181 logger.info("%s reused job %s", self.arvrunner.label(self), response["uuid"])
182 # Give read permission to the desired project on reused jobs
183 if response["owner_uuid"] != self.arvrunner.project_uuid:
185 self.arvrunner.api.links().create(body={
186 'link_class': 'permission',
188 'tail_uuid': self.arvrunner.project_uuid,
189 'head_uuid': response["uuid"],
190 }).execute(num_retries=self.arvrunner.num_retries)
191 except ApiError as e:
192 # The user might not have "manage" access on the job: log
193 # a message and continue.
194 logger.info("Creating read permission on job %s: %s",
198 logger.info("%s %s is %s", self.arvrunner.label(self), response["uuid"], response["state"])
199 except Exception as e:
200 logger.exception("%s error" % (self.arvrunner.label(self)))
201 self.output_callback({}, "permanentFail")
203 def update_pipeline_component(self, record):
204 with self.arvrunner.workflow_eval_lock:
205 if self.arvrunner.pipeline:
206 self.arvrunner.pipeline["components"][self.name] = {"job": record}
207 with Perf(metrics, "update_pipeline_component %s" % self.name):
208 self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().update(
209 uuid=self.arvrunner.pipeline["uuid"],
211 "components": self.arvrunner.pipeline["components"]
212 }).execute(num_retries=self.arvrunner.num_retries)
213 if self.arvrunner.uuid:
215 job = self.arvrunner.api.jobs().get(uuid=self.arvrunner.uuid).execute()
217 components = job["components"]
218 components[self.name] = record["uuid"]
219 self.arvrunner.api.jobs().update(
220 uuid=self.arvrunner.uuid,
222 "components": components
223 }).execute(num_retries=self.arvrunner.num_retries)
224 except Exception as e:
225 logger.info("Error adding to components: %s", e)
227 def done(self, record):
229 self.update_pipeline_component(record)
234 if record["state"] == "Complete":
235 processStatus = "success"
237 processStatus = "permanentFail"
242 with Perf(metrics, "inspect log %s" % self.name):
243 logc = arvados.collection.CollectionReader(record["log"],
244 api_client=self.arvrunner.api,
245 keep_client=self.arvrunner.keep_client,
246 num_retries=self.arvrunner.num_retries)
247 log = logc.open(logc.keys()[0])
254 # Determine the tmpdir, outdir and keep paths from
255 # the job run. Unfortunately, we can't take the first
256 # values we find (which are expected to be near the
257 # top) and stop scanning because if the node fails and
258 # the job restarts on a different node these values
259 # will different runs, and we need to know about the
260 # final run that actually produced output.
261 g = crunchrunner_re.match(l)
263 dirs[g.group(1)] = g.group(2)
265 if processStatus == "permanentFail":
266 done.logtail(logc, logger.error, "%s (%s) error log:" % (self.arvrunner.label(self), record["uuid"]), maxlen=40)
268 with Perf(metrics, "output collection %s" % self.name):
269 outputs = done.done(self, record, dirs["tmpdir"],
270 dirs["outdir"], dirs["keep"])
271 except WorkflowException as e:
272 logger.error("%s unable to collect output from %s:\n%s",
273 self.arvrunner.label(self), record["output"], e, exc_info=(e if self.arvrunner.debug else False))
274 processStatus = "permanentFail"
275 except Exception as e:
276 logger.exception("Got unknown exception while collecting output for job %s:", self.name)
277 processStatus = "permanentFail"
279 # Note: Currently, on error output_callback is expecting an empty dict,
280 # anything else will fail.
281 if not isinstance(outputs, dict):
282 logger.error("Unexpected output type %s '%s'", type(outputs), outputs)
284 processStatus = "permanentFail"
286 self.output_callback(outputs, processStatus)
289 class RunnerJob(Runner):
290 """Submit and manage a Crunch job that runs crunch_scripts/cwl-runner."""
292 def arvados_job_spec(self, debug=False):
293 """Create an Arvados job specification for this workflow.
295 The returned dict can be used to create a job (i.e., passed as
296 the +body+ argument to jobs().create()), or as a component in
297 a pipeline template or pipeline instance.
300 if self.tool.tool["id"].startswith("keep:"):
301 self.job_order["cwl:tool"] = self.tool.tool["id"][5:]
303 packed = packed_workflow(self.arvrunner, self.tool, self.merged_map)
304 wf_pdh = upload_workflow_collection(self.arvrunner, self.name, packed)
305 self.job_order["cwl:tool"] = "%s/workflow.cwl#main" % wf_pdh
307 adjustDirObjs(self.job_order, trim_listing)
308 visit_class(self.job_order, ("File", "Directory"), trim_anonymous_location)
309 visit_class(self.job_order, ("File", "Directory"), remove_redundant_fields)
312 self.job_order["arv:output_name"] = self.output_name
315 self.job_order["arv:output_tags"] = self.output_tags
317 self.job_order["arv:enable_reuse"] = self.enable_reuse
320 self.job_order["arv:on_error"] = self.on_error
323 self.job_order["arv:debug"] = True
326 "script": "cwl-runner",
327 "script_version": "master",
328 "minimum_script_version": "570509ab4d2ef93d870fd2b1f2eab178afb1bad9",
329 "repository": "arvados",
330 "script_parameters": self.job_order,
331 "runtime_constraints": {
332 "docker_image": arvados_jobs_image(self.arvrunner, self.jobs_image),
333 "min_ram_mb_per_node": self.submit_runner_ram
337 def run(self, runtimeContext):
338 job_spec = self.arvados_job_spec(runtimeContext.debug)
340 job_spec.setdefault("owner_uuid", self.arvrunner.project_uuid)
342 job = self.arvrunner.api.jobs().create(
344 find_or_create=self.enable_reuse
345 ).execute(num_retries=self.arvrunner.num_retries)
347 for k,v in job_spec["script_parameters"].items():
348 if v is False or v is None or isinstance(v, dict):
349 job_spec["script_parameters"][k] = {"value": v}
351 del job_spec["owner_uuid"]
352 job_spec["job"] = job
355 "owner_uuid": self.arvrunner.project_uuid,
358 "cwl-runner": job_spec,
360 "state": "RunningOnServer",
362 if not self.enable_reuse:
363 instance_spec["properties"] = {"run_options": {"enable_job_reuse": False}}
365 self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().create(
366 body=instance_spec).execute(num_retries=self.arvrunner.num_retries)
367 logger.info("Created pipeline %s", self.arvrunner.pipeline["uuid"])
369 if runtimeContext.wait is False:
370 self.uuid = self.arvrunner.pipeline["uuid"]
373 self.uuid = job["uuid"]
374 self.arvrunner.process_submitted(self)
377 class RunnerTemplate(object):
378 """An Arvados pipeline template that invokes a CWL workflow."""
380 type_to_dataclass = {
381 'boolean': 'boolean',
383 'Directory': 'Collection',
389 def __init__(self, runner, tool, job_order, enable_reuse, uuid,
390 submit_runner_ram=0, name=None, merged_map=None):
393 self.job = RunnerJob(
397 enable_reuse=enable_reuse,
400 submit_runner_ram=submit_runner_ram,
402 merged_map=merged_map)
405 def pipeline_component_spec(self):
406 """Return a component that Workbench and a-r-p-i will understand.
408 Specifically, translate CWL input specs to Arvados pipeline
409 format, like {"dataclass":"File","value":"xyz"}.
412 spec = self.job.arvados_job_spec()
414 # Most of the component spec is exactly the same as the job
415 # spec (script, script_version, etc.).
416 # spec['script_parameters'] isn't right, though. A component
417 # spec's script_parameters hash is a translation of
418 # self.tool.tool['inputs'] with defaults/overrides taken from
419 # the job order. So we move the job parameters out of the way
420 # and build a new spec['script_parameters'].
421 job_params = spec['script_parameters']
422 spec['script_parameters'] = {}
424 for param in self.tool.tool['inputs']:
425 param = copy.deepcopy(param)
427 # Data type and "required" flag...
428 types = param['type']
429 if not isinstance(types, list):
431 param['required'] = 'null' not in types
432 non_null_types = [t for t in types if t != "null"]
433 if len(non_null_types) == 1:
434 the_type = [c for c in non_null_types][0]
436 if isinstance(the_type, basestring):
437 dataclass = self.type_to_dataclass.get(the_type)
439 param['dataclass'] = dataclass
440 # Note: If we didn't figure out a single appropriate
441 # dataclass, we just left that attribute out. We leave
442 # the "type" attribute there in any case, which might help
445 # Title and description...
446 title = param.pop('label', '')
447 descr = param.pop('doc', '').rstrip('\n')
449 param['title'] = title
451 param['description'] = descr
453 # Fill in the value from the current job order, if any.
454 param_id = shortname(param.pop('id'))
455 value = job_params.get(param_id)
458 elif not isinstance(value, dict):
459 param['value'] = value
460 elif param.get('dataclass') in ('File', 'Collection') and value.get('location'):
461 param['value'] = value['location'][5:]
463 spec['script_parameters'][param_id] = param
464 spec['script_parameters']['cwl:tool'] = job_params['cwl:tool']
470 self.job.name: self.pipeline_component_spec(),
472 "name": self.job.name,
474 if self.runner.project_uuid:
475 body["owner_uuid"] = self.runner.project_uuid
477 self.runner.api.pipeline_templates().update(
478 uuid=self.uuid, body=body).execute(
479 num_retries=self.runner.num_retries)
480 logger.info("Updated template %s", self.uuid)
482 self.uuid = self.runner.api.pipeline_templates().create(
483 body=body, ensure_unique_name=True).execute(
484 num_retries=self.runner.num_retries)['uuid']
485 logger.info("Created template %s", self.uuid)