import arvados_cwl.util
from .arvcontainer import RunnerContainer
-from .runner import Runner, upload_docker, upload_job_order, upload_workflow_deps
+from .runner import Runner, upload_docker, upload_job_order, upload_workflow_deps, make_builder
from .arvtool import ArvadosCommandTool, validate_cluster_target, ArvadosExpressionTool
from .arvworkflow import ArvadosWorkflow, upload_workflow
from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver, CollectionCache, pdh_size
runtimeContext.tmpdir_prefix = "tmp"
runtimeContext.work_api = self.work_api
+ if not self.output_name:
+ self.output_name = "Output from workflow %s" % runtimeContext.name
+
if self.work_api == "containers":
if self.ignore_docker_for_reuse:
raise Exception("--ignore-docker-for-reuse not supported with containers API.")
if workbench2 or workbench1:
logger.info("Output at %scollections/%s", workbench2 or workbench1, tool.final_output)
else:
- if self.output_name is None:
- self.output_name = "Output of %s" % (shortname(tool.tool["id"]))
if self.output_tags is None:
self.output_tags = ""
output_properties = {}
output_properties_req, _ = tool.get_requirement("http://arvados.org/cwl#OutputCollectionProperties")
if output_properties_req:
+ builder = make_builder(job_order, tool.hints, tool.requirements, runtimeContext, tool.metadata)
for pr in output_properties_req["outputProperties"]:
- output_properties[pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"])
+ output_properties[pr["propertyName"]] = builder.do_eval(pr["propertyValue"])
self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, storage_classes,
self.output_tags, output_properties,