6 from cwltool.process import get_feature, shortname
7 from cwltool.errors import WorkflowException
8 from cwltool.draft2tool import revmap_file, CommandLineTool
9 from cwltool.load_tool import fetch_document
10 from cwltool.builder import Builder
12 import arvados.collection
14 from .arvdocker import arv_docker_get_image
15 from .runner import Runner
16 from .pathmapper import InitialWorkDirPathMapper
17 from .perf import Perf
20 logger = logging.getLogger('arvados.cwl-runner')
21 metrics = logging.getLogger('arvados.cwl-runner.metrics')
23 tmpdirre = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.tmpdir\)=(.*)")
24 outdirre = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.outdir\)=(.*)")
25 keepre = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.keep\)=(.*)")
27 class ArvadosJob(object):
28 """Submit and manage a Crunch job for executing a CWL CommandLineTool."""
30 def __init__(self, runner):
31 self.arvrunner = runner
35 def run(self, dry_run=False, pull_image=True, **kwargs):
37 "command": self.command_line
39 runtime_constraints = {}
41 with Perf(metrics, "generatefiles %s" % self.name):
42 if self.generatefiles["listing"]:
43 vwd = arvados.collection.Collection(api_client=self.arvrunner.api,
44 keep_client=self.arvrunner.keep_client,
45 num_retries=self.arvrunner.num_retries)
46 script_parameters["task.vwd"] = {}
47 generatemapper = InitialWorkDirPathMapper([self.generatefiles], "", "",
50 with Perf(metrics, "createfiles %s" % self.name):
51 for f, p in generatemapper.items():
52 if p.type == "CreateFile":
53 with vwd.open(p.target, "w") as n:
54 n.write(p.resolved.encode("utf-8"))
56 with Perf(metrics, "generatefiles.save_new %s" % self.name):
59 for f, p in generatemapper.items():
61 script_parameters["task.vwd"][p.target] = p.resolved
62 if p.type == "CreateFile":
63 script_parameters["task.vwd"][p.target] = "$(task.keep)/%s/%s" % (vwd.portable_data_hash(), p.target)
65 script_parameters["task.env"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
67 script_parameters["task.env"].update(self.environment)
70 script_parameters["task.stdin"] = self.stdin
73 script_parameters["task.stdout"] = self.stdout
76 script_parameters["task.stderr"] = self.stderr
79 script_parameters["task.successCodes"] = self.successCodes
80 if self.temporaryFailCodes:
81 script_parameters["task.temporaryFailCodes"] = self.temporaryFailCodes
82 if self.permanentFailCodes:
83 script_parameters["task.permanentFailCodes"] = self.permanentFailCodes
85 with Perf(metrics, "arv_docker_get_image %s" % self.name):
86 (docker_req, docker_is_req) = get_feature(self, "DockerRequirement")
87 if docker_req and kwargs.get("use_container") is not False:
88 runtime_constraints["docker_image"] = arv_docker_get_image(self.arvrunner.api, docker_req, pull_image, self.arvrunner.project_uuid)
90 runtime_constraints["docker_image"] = "arvados/jobs"
92 resources = self.builder.resources
93 if resources is not None:
94 runtime_constraints["min_cores_per_node"] = resources.get("cores", 1)
95 runtime_constraints["min_ram_mb_per_node"] = resources.get("ram")
96 runtime_constraints["min_scratch_mb_per_node"] = resources.get("tmpdirSize", 0) + resources.get("outdirSize", 0)
98 runtime_req, _ = get_feature(self, "http://arvados.org/cwl#RuntimeConstraints")
100 if "keep_cache" in runtime_req:
101 runtime_constraints["keep_cache_mb_per_task"] = runtime_req["keep_cache"]
102 if "outputDirType" in runtime_req:
103 if runtime_req["outputDirType"] == "local_output_dir":
104 script_parameters["task.keepTmpOutput"] = False
105 elif runtime_req["outputDirType"] == "keep_output_dir":
106 script_parameters["task.keepTmpOutput"] = True
108 filters = [["repository", "=", "arvados"],
109 ["script", "=", "crunchrunner"],
110 ["script_version", "in git", "9e5b98e8f5f4727856b53447191f9c06e3da2ba6"]]
111 if not self.arvrunner.ignore_docker_for_reuse:
112 filters.append(["docker_image_locator", "in docker", runtime_constraints["docker_image"]])
115 with Perf(metrics, "create %s" % self.name):
116 response = self.arvrunner.api.jobs().create(
118 "owner_uuid": self.arvrunner.project_uuid,
119 "script": "crunchrunner",
120 "repository": "arvados",
121 "script_version": "master",
122 "minimum_script_version": "9e5b98e8f5f4727856b53447191f9c06e3da2ba6",
123 "script_parameters": {"tasks": [script_parameters]},
124 "runtime_constraints": runtime_constraints
127 find_or_create=kwargs.get("enable_reuse", True)
128 ).execute(num_retries=self.arvrunner.num_retries)
130 self.arvrunner.processes[response["uuid"]] = self
132 self.update_pipeline_component(response)
134 logger.info("Job %s (%s) is %s", self.name, response["uuid"], response["state"])
136 if response["state"] in ("Complete", "Failed", "Cancelled"):
137 with Perf(metrics, "done %s" % self.name):
139 except Exception as e:
140 logger.error("Got error %s" % str(e))
141 self.output_callback({}, "permanentFail")
143 def update_pipeline_component(self, record):
144 if self.arvrunner.pipeline:
145 self.arvrunner.pipeline["components"][self.name] = {"job": record}
146 with Perf(metrics, "update_pipeline_component %s" % self.name):
147 self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().update(uuid=self.arvrunner.pipeline["uuid"],
149 "components": self.arvrunner.pipeline["components"]
150 }).execute(num_retries=self.arvrunner.num_retries)
151 if self.arvrunner.uuid:
153 job = self.arvrunner.api.jobs().get(uuid=self.arvrunner.uuid).execute()
155 components = job["components"]
156 components[self.name] = record["uuid"]
157 self.arvrunner.api.jobs().update(uuid=self.arvrunner.uuid,
159 "components": components
160 }).execute(num_retries=self.arvrunner.num_retries)
161 except Exception as e:
162 logger.info("Error adding to components: %s", e)
164 def done(self, record):
166 self.update_pipeline_component(record)
171 if record["state"] == "Complete":
172 processStatus = "success"
174 processStatus = "permanentFail"
179 with Perf(metrics, "inspect log %s" % self.name):
180 logc = arvados.collection.CollectionReader(record["log"],
181 api_client=self.arvrunner.api,
182 keep_client=self.arvrunner.keep_client,
183 num_retries=self.arvrunner.num_retries)
184 log = logc.open(logc.keys()[0])
189 # Determine the tmpdir, outdir and keepdir paths from
190 # the job run. Unfortunately, we can't take the first
191 # values we find (which are expected to be near the
192 # top) and stop scanning because if the node fails and
193 # the job restarts on a different node these values
194 # will different runs, and we need to know about the
195 # final run that actually produced output.
197 g = tmpdirre.match(l)
200 g = outdirre.match(l)
207 with Perf(metrics, "output collection %s" % self.name):
208 outputs = done.done(self, record, tmpdir, outdir, keepdir)
209 except WorkflowException as e:
210 logger.error("Error while collecting job outputs:\n%s", e, exc_info=(e if self.arvrunner.debug else False))
211 processStatus = "permanentFail"
213 except Exception as e:
214 logger.exception("Got unknown exception while collecting job outputs:")
215 processStatus = "permanentFail"
218 self.output_callback(outputs, processStatus)
220 del self.arvrunner.processes[record["uuid"]]
223 class RunnerJob(Runner):
224 """Submit and manage a Crunch job that runs crunch_scripts/cwl-runner."""
226 def arvados_job_spec(self, dry_run=False, pull_image=True, **kwargs):
227 """Create an Arvados job specification for this workflow.
229 The returned dict can be used to create a job (i.e., passed as
230 the +body+ argument to jobs().create()), or as a component in
231 a pipeline template or pipeline instance.
234 workflowmapper = super(RunnerJob, self).arvados_job_spec(dry_run=dry_run, pull_image=pull_image, **kwargs)
236 self.job_order["cwl:tool"] = workflowmapper.mapper(self.tool.tool["id"]).target[5:]
238 self.job_order["arv:output_name"] = self.output_name
240 "script": "cwl-runner",
241 "script_version": "master",
242 "repository": "arvados",
243 "script_parameters": self.job_order,
244 "runtime_constraints": {
245 "docker_image": "arvados/jobs"
249 def run(self, *args, **kwargs):
250 job_spec = self.arvados_job_spec(*args, **kwargs)
251 job_spec.setdefault("owner_uuid", self.arvrunner.project_uuid)
253 response = self.arvrunner.api.jobs().create(
255 find_or_create=self.enable_reuse
256 ).execute(num_retries=self.arvrunner.num_retries)
258 self.uuid = response["uuid"]
259 self.arvrunner.processes[self.uuid] = self
261 logger.info("Submitted job %s", response["uuid"])
263 if kwargs.get("submit"):
264 self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().create(
266 "owner_uuid": self.arvrunner.project_uuid,
267 "name": shortname(self.tool.tool["id"]),
268 "components": {"cwl-runner": {"job": {"uuid": self.uuid, "state": response["state"]} } },
269 "state": "RunningOnClient"}).execute(num_retries=self.arvrunner.num_retries)
271 if response["state"] in ("Complete", "Failed", "Cancelled"):
275 class RunnerTemplate(object):
276 """An Arvados pipeline template that invokes a CWL workflow."""
278 type_to_dataclass = {
279 'boolean': 'boolean',
281 'Directory': 'Collection',
287 def __init__(self, runner, tool, job_order, enable_reuse):
290 self.job = RunnerJob(
294 enable_reuse=enable_reuse,
297 def pipeline_component_spec(self):
298 """Return a component that Workbench and a-r-p-i will understand.
300 Specifically, translate CWL input specs to Arvados pipeline
301 format, like {"dataclass":"File","value":"xyz"}.
303 spec = self.job.arvados_job_spec()
305 # Most of the component spec is exactly the same as the job
306 # spec (script, script_version, etc.).
307 # spec['script_parameters'] isn't right, though. A component
308 # spec's script_parameters hash is a translation of
309 # self.tool.tool['inputs'] with defaults/overrides taken from
310 # the job order. So we move the job parameters out of the way
311 # and build a new spec['script_parameters'].
312 job_params = spec['script_parameters']
313 spec['script_parameters'] = {}
315 for param in self.tool.tool['inputs']:
316 param = copy.deepcopy(param)
318 # Data type and "required" flag...
319 types = param['type']
320 if not isinstance(types, list):
322 param['required'] = 'null' not in types
323 non_null_types = set(types) - set(['null'])
324 if len(non_null_types) == 1:
325 the_type = [c for c in non_null_types][0]
326 dataclass = self.type_to_dataclass.get(the_type)
328 param['dataclass'] = dataclass
329 # Note: If we didn't figure out a single appropriate
330 # dataclass, we just left that attribute out. We leave
331 # the "type" attribute there in any case, which might help
334 # Title and description...
335 title = param.pop('label', '')
336 descr = param.pop('doc', '').rstrip('\n')
338 param['title'] = title
340 param['description'] = descr
342 # Fill in the value from the current job order, if any.
343 param_id = shortname(param.pop('id'))
344 value = job_params.get(param_id)
347 elif not isinstance(value, dict):
348 param['value'] = value
349 elif param.get('dataclass') in ('File', 'Collection') and value.get('location'):
350 param['value'] = value['location'][5:]
352 spec['script_parameters'][param_id] = param
353 spec['script_parameters']['cwl:tool'] = job_params['cwl:tool']
357 job_spec = self.pipeline_component_spec()
358 response = self.runner.api.pipeline_templates().create(body={
360 self.job.name: job_spec,
362 "name": self.job.name,
363 "owner_uuid": self.runner.project_uuid,
364 }, ensure_unique_name=True).execute(num_retries=self.runner.num_retries)
365 self.uuid = response["uuid"]
366 logger.info("Created template %s", self.uuid)