from cwltool.errors import WorkflowException
from cwltool.process import get_feature, UnsupportedRequirement, shortname
-from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
+from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
from cwltool.utils import aslist
import arvados.collection
from .arvdocker import arv_docker_get_image
from . import done
-from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location
+from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location, remove_redundant_fields
from .fsaccess import CollectionFetcher
from .pathmapper import NoFollowPathMapper, trim_listing
from .perf import Perf
container_request["output_ttl"] = self.output_ttl
container_request["mounts"] = mounts
container_request["runtime_constraints"] = runtime_constraints
- container_request["use_existing"] = kwargs.get("enable_reuse", True)
container_request["scheduling_parameters"] = scheduling_parameters
+ enable_reuse = kwargs.get("enable_reuse", True)
+ if enable_reuse:
+ reuse_req, _ = get_feature(self, "http://arvados.org/cwl#ReuseRequirement")
+ if reuse_req:
+ enable_reuse = reuse_req["enableReuse"]
+ container_request["use_existing"] = enable_reuse
+
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)
"""
adjustDirObjs(self.job_order, trim_listing)
- adjustFileObjs(self.job_order, trim_anonymous_location)
- adjustDirObjs(self.job_order, trim_anonymous_location)
+ visit_class(self.job_order, ("File", "Directory"), trim_anonymous_location)
+ visit_class(self.job_order, ("File", "Directory"), remove_redundant_fields)
container_req = {
"owner_uuid": self.arvrunner.project_uuid,
"ram": 1024*1024 * self.submit_runner_ram,
"API": True
},
+ "use_existing": self.enable_reuse,
"properties": {}
}
if self.arvrunner.trash_intermediate:
command.append("--trash-intermediate")
+ if self.arvrunner.project_uuid:
+ command.append("--project-uuid="+self.arvrunner.project_uuid)
+
command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
container_req["command"] = command