import json
import os
+import ruamel.yaml as yaml
+
from cwltool.errors import WorkflowException
from cwltool.process import get_feature, UnsupportedRequirement, shortname
from cwltool.pathmapper import adjustFiles
from .arvdocker import arv_docker_get_image
from . import done
from .runner import Runner, arvados_jobs_image
+from .fsaccess import CollectionFetcher
logger = logging.getLogger('arvados.cwl-runner')
}
if self.generatefiles["listing"]:
- raise UnsupportedRequirement("Generate files not supported")
+ raise UnsupportedRequirement("InitialWorkDirRequirement not supported with --api=containers")
container_request["environment"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
if self.environment:
body=container_request
).execute(num_retries=self.arvrunner.num_retries)
- self.arvrunner.processes[response["container_uuid"]] = self
-
- container = self.arvrunner.api.containers().get(
- uuid=response["container_uuid"]
- ).execute(num_retries=self.arvrunner.num_retries)
+ self.arvrunner.processes[response["uuid"]] = self
- logger.info("Container request %s (%s) state is %s with container %s %s", self.name, response["uuid"], response["state"], container["uuid"], container["state"])
+ logger.info("Container request %s (%s) state is %s", self.name, response["uuid"], response["state"])
- if container["state"] in ("Complete", "Cancelled"):
- self.done(container)
+ if response["state"] == "Final":
+ self.done(response)
except Exception as e:
logger.error("Got error %s" % str(e))
self.output_callback({}, "permanentFail")
def done(self, record):
try:
- if record["state"] == "Complete":
- rcode = record["exit_code"]
+ container = self.arvrunner.api.containers().get(
+ uuid=record["container_uuid"]
+ ).execute(num_retries=self.arvrunner.num_retries)
+ if container["state"] == "Complete":
+ rcode = container["exit_code"]
if self.successCodes and rcode in self.successCodes:
processStatus = "success"
elif self.temporaryFailCodes and rcode in self.temporaryFailCodes:
else:
processStatus = "permanentFail"
- try:
- outputs = {}
- if record["output"]:
- outputs = done.done(self, record, "/tmp", self.outdir, "/keep")
- except WorkflowException as e:
- logger.error("Error while collecting container outputs:\n%s", e, exc_info=(e if self.arvrunner.debug else False))
- processStatus = "permanentFail"
- except Exception as e:
- logger.exception("Got unknown exception while collecting job outputs:")
- processStatus = "permanentFail"
+ 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")
self.output_callback(outputs, processStatus)
finally:
del self.arvrunner.processes[record["uuid"]]
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"
- command = ["arvados-cwl-runner", "--local", "--api=containers"]
- if self.output_name:
- command.append("--output-name=" + self.output_name)
-
- if self.output_tags:
- command.append("--output-tags=" + self.output_tags)
-
- if self.enable_reuse:
- command.append("--enable-reuse")
- else:
- command.append("--disable-reuse")
-
- command.extend([workflowpath, jobpath])
-
- return {
- "command": command,
+ container_req = {
"owner_uuid": self.arvrunner.project_uuid,
"name": self.name,
"output_path": "/var/spool/cwl",
"state": "Committed",
"container_image": arvados_jobs_image(self.arvrunner),
"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()
},
"runtime_constraints": {
"vcpus": 1,
- "ram": 1024*1024*256,
+ "ram": 1024*1024 * self.submit_runner_ram,
"API": True
}
}
+ workflowcollection = workflowmapper.mapper(self.tool.tool["id"])[1]
+ if workflowcollection.startswith("keep:"):
+ workflowcollection = workflowcollection[5:workflowcollection.index('/')]
+ workflowname = os.path.basename(self.tool.tool["id"])
+ workflowpath = "/var/lib/cwl/workflow/%s" % workflowname
+ container_req["mounts"]["/var/lib/cwl/workflow"] = {
+ "kind": "collection",
+ "portable_data_hash": "%s" % workflowcollection
+ }
+ 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))
+ container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
+ "kind": "json",
+ "json": wfobj
+ }
+
+ command = ["arvados-cwl-runner", "--local", "--api=containers"]
+ if self.output_name:
+ command.append("--output-name=" + self.output_name)
+
+ if self.output_tags:
+ command.append("--output-tags=" + self.output_tags)
+
+ if self.enable_reuse:
+ command.append("--enable-reuse")
+ else:
+ command.append("--disable-reuse")
+
+ command.extend([workflowpath, jobpath])
+
+ container_req["command"] = command
+
+ return container_req
+
+
def run(self, *args, **kwargs):
kwargs["keepprefix"] = "keep:"
job_spec = self.arvados_job_spec(*args, **kwargs)
).execute(num_retries=self.arvrunner.num_retries)
self.uuid = response["uuid"]
- self.arvrunner.processes[response["container_uuid"]] = self
+ self.arvrunner.processes[response["uuid"]] = self
logger.info("Submitted container %s", response["uuid"])
- if response["state"] in ("Complete", "Failed", "Cancelled"):
+ if response["state"] == "Final":
self.done(response)
+
+ def done(self, record):
+ try:
+ container = self.arvrunner.api.containers().get(
+ uuid=record["container_uuid"]
+ ).execute(num_retries=self.arvrunner.num_retries)
+ except Exception as e:
+ logger.exception("While getting runner container: %s", 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"]]