+ del self.arvrunner.processes[record["uuid"]]
+
+
+class RunnerContainer(Runner):
+ """Submit and manage a container that runs arvados-cwl-runner."""
+
+ def arvados_job_spec(self, dry_run=False, pull_image=True, **kwargs):
+ """Create an Arvados container request for this workflow.
+
+ The returned dict can be used to create a container passed as
+ the +body+ argument to container_requests().create().
+ """
+
+ 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) 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)
+
+ workflowname = os.path.basename(self.tool.tool["id"])
+ workflowpath = "/var/lib/cwl/workflow/%s" % workflowname
+ workflowcollection = workflowmapper.mapper(self.tool.tool["id"])[1]
+ workflowcollection = workflowcollection[5:workflowcollection.index('/')]
+ jobpath = "/var/lib/cwl/job/cwl.input.json"
+
+ container_image = arv_docker_get_image(self.arvrunner.api,
+ {"dockerImageId": "arvados/jobs"},
+ pull_image,
+ self.arvrunner.project_uuid)
+
+ return {
+ "command": ["arvados-cwl-runner", "--local", "--api=containers", workflowpath, jobpath],
+ "owner_uuid": self.arvrunner.project_uuid,
+ "name": self.name,
+ "output_path": "/var/spool/cwl",
+ "cwd": "/var/spool/cwl",
+ "priority": 1,
+ "state": "Committed",
+ "container_image": container_image,
+ "mounts": {
+ "/var/lib/cwl/workflow": {
+ "kind": "collection",
+ "portable_data_hash": "%s" % workflowcollection
+ },
+ jobpath: {
+ "kind": "collection",
+ "portable_data_hash": "%s/cwl.input.json" % jobobj.portable_data_hash()
+ },
+ "stdout": {
+ "kind": "file",
+ "path": "/var/spool/cwl/cwl.output.json"
+ },
+ "/var/spool/cwl": {
+ "kind": "collection",
+ "writable": True
+ }
+ },
+ "runtime_constraints": {
+ "vcpus": 1,
+ "ram": 1024*1024*256,
+ "API": True
+ }
+ }
+
+ def run(self, *args, **kwargs):
+ kwargs["keepprefix"] = "keep:"
+ job_spec = self.arvados_job_spec(*args, **kwargs)
+ job_spec.setdefault("owner_uuid", self.arvrunner.project_uuid)
+
+ response = self.arvrunner.api.container_requests().create(
+ body=job_spec
+ ).execute(num_retries=self.arvrunner.num_retries)
+
+ self.uuid = response["uuid"]
+ self.arvrunner.processes[response["container_uuid"]] = self
+
+ logger.info("Submitted container %s", response["uuid"])
+
+ if response["state"] in ("Complete", "Failed", "Cancelled"):
+ self.done(response)