"output_path": self.outdir,
"cwd": self.outdir,
"priority": 1,
- "state": "Committed"
+ "state": "Committed",
+ "properties": {}
}
runtime_constraints = {}
mounts = {
container_request["use_existing"] = kwargs.get("enable_reuse", True)
container_request["scheduling_parameters"] = scheduling_parameters
+ if kwargs.get("runnerjob", "").startswith("arvwf:"):
+ wfuuid = kwargs["runnerjob"][6:kwargs["runnerjob"].index("#")]
+ wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(num_retries=self.arvrunner.num_retries)
+ if container_request["name"] == "main":
+ container_request["name"] = wfrecord["name"]
+ container_request["properties"]["template_uuid"] = wfuuid
+
try:
response = self.arvrunner.api.container_requests().create(
body=container_request
).execute(num_retries=self.arvrunner.num_retries)
- self.arvrunner.processes[response["uuid"]] = self
+ self.uuid = response["uuid"]
+ self.arvrunner.processes[self.uuid] = self
- logger.info("Container request %s (%s) state is %s", self.name, response["uuid"], response["state"])
+ logger.info("%s %s state is %s", self.arvrunner.label(self), response["uuid"], response["state"])
if response["state"] == "Final":
self.done(response)
except Exception as e:
- logger.error("Got error %s" % str(e))
+ logger.error("%s got error %s" % (self.arvrunner.label(self), str(e)))
self.output_callback({}, "permanentFail")
def done(self, record):
else:
processStatus = "permanentFail"
- outputs = {}
+ if processStatus == "permanentFail":
+ logc = arvados.collection.CollectionReader(container["log"],
+ api_client=self.arvrunner.api,
+ keep_client=self.arvrunner.keep_client,
+ num_retries=self.arvrunner.num_retries)
+ done.logtail(logc, logger, "%s error log:" % self.arvrunner.label(self))
+ outputs = {}
if container["output"]:
- try:
- outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
- except Exception as e:
- logger.error("Got error %s" % str(e))
- self.output_callback({}, "permanentFail")
+ outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
+ except WorkflowException as e:
+ logger.error("%s unable to collect output from %s:\n%s",
+ self.arvrunner.label(self), container["output"], e, exc_info=(e if self.arvrunner.debug else False))
+ processStatus = "permanentFail"
+ except Exception as e:
+ logger.exception("%s while getting output object: %s", self.arvrunner.label(self), e)
+ self.output_callback({}, "permanentFail")
+ else:
self.output_callback(outputs, processStatus)
finally:
- del self.arvrunner.processes[record["uuid"]]
+ if record["uuid"] in self.arvrunner.processes:
+ del self.arvrunner.processes[record["uuid"]]
class RunnerContainer(Runner):
workflowmapper = super(RunnerContainer, self).arvados_job_spec(dry_run=dry_run, pull_image=pull_image, **kwargs)
- with arvados.collection.Collection(api_client=self.arvrunner.api,
- keep_client=self.arvrunner.keep_client,
- num_retries=self.arvrunner.num_retries) as jobobj:
- with jobobj.open("cwl.input.json", "w") as f:
- json.dump(self.job_order, f, sort_keys=True, indent=4)
- jobobj.save_new(owner_uuid=self.arvrunner.project_uuid)
-
- jobpath = "/var/lib/cwl/job/cwl.input.json"
-
container_req = {
"owner_uuid": self.arvrunner.project_uuid,
"name": self.name,
"state": "Committed",
"container_image": arvados_jobs_image(self.arvrunner),
"mounts": {
- jobpath: {
- "kind": "collection",
- "portable_data_hash": "%s/cwl.input.json" % jobobj.portable_data_hash()
+ "/var/lib/cwl/cwl.input.json": {
+ "kind": "json",
+ "content": self.job_order
},
"stdout": {
"kind": "file",
"vcpus": 1,
"ram": 1024*1024 * self.submit_runner_ram,
"API": True
- }
+ },
+ "properties": {}
}
workflowcollection = workflowmapper.mapper(self.tool.tool["id"])[1]
}
elif workflowcollection.startswith("arvwf:"):
workflowpath = "/var/lib/cwl/workflow.json#main"
- fetcher = CollectionFetcher({}, None,
- api_client=self.arvrunner.api,
- keep_client=self.arvrunner.keep_client)
- wfobj = yaml.safe_load(fetcher.fetch_text(workflowcollection))
+ wfuuid = workflowcollection[6:workflowcollection.index("#")]
+ wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(num_retries=self.arvrunner.num_retries)
+ wfobj = yaml.safe_load(wfrecord["definition"])
+ if container_req["name"].startswith("arvwf:"):
+ container_req["name"] = wfrecord["name"]
container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
"kind": "json",
"json": wfobj
}
+ container_req["properties"]["template_uuid"] = wfuuid
- command = ["arvados-cwl-runner", "--local", "--api=containers"]
+ command = ["arvados-cwl-runner", "--local", "--api=containers", "--no-log-timestamps"]
if self.output_name:
command.append("--output-name=" + self.output_name)
if self.output_tags:
command.append("--output-tags=" + self.output_tags)
+ if kwargs.get("debug"):
+ command.append("--debug")
+
if self.enable_reuse:
command.append("--enable-reuse")
else:
command.append("--disable-reuse")
- command.extend([workflowpath, jobpath])
+ command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
container_req["command"] = command
).execute(num_retries=self.arvrunner.num_retries)
self.uuid = response["uuid"]
- self.arvrunner.processes[response["uuid"]] = self
+ self.arvrunner.processes[self.uuid] = self
- logger.info("Submitted container %s", response["uuid"])
+ logger.info("%s submitted container %s", self.arvrunner.label(self), response["uuid"])
if response["state"] == "Final":
self.done(response)
uuid=record["container_uuid"]
).execute(num_retries=self.arvrunner.num_retries)
except Exception as e:
- logger.exception("While getting runner container: %s", e)
+ logger.exception("%s while getting runner container: %s", self.arvrunner.label(self), e)
self.arvrunner.output_callback({}, "permanentFail")
- del self.arvrunner.processes[record["uuid"]]
else:
super(RunnerContainer, self).done(container)
finally:
- del self.arvrunner.processes[record["uuid"]]
+ if record["uuid"] in self.arvrunner.processes:
+ del self.arvrunner.processes[record["uuid"]]
projects / arvados.git / blobdiff