class RunnerContainer(Runner):
"""Submit and manage a container that runs arvados-cwl-runner."""
- def arvados_job_spec(self, runtimeContext):
+ def arvados_job_spec(self, runtimeContext, git_info):
"""Create an Arvados container request for this workflow.
The returned dict can be used to create a container passed as
"portable_data_hash": "%s" % workflowcollection
}
else:
- packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map, runtimeContext)
+ packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map, runtimeContext, git_info)
workflowpath = "/var/lib/cwl/workflow.json#main"
container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
"kind": "json",
if self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
+ container_req["properties"].update({k.replace("http://arvados.org/cwl#", "arv:"): v for k, v in git_info.items()})
+
properties_req, _ = self.embedded_tool.get_requirement("http://arvados.org/cwl#ProcessProperties")
if properties_req:
builder = make_builder(self.job_order, self.embedded_tool.hints, self.embedded_tool.requirements, runtimeContext, self.embedded_tool.metadata)
def run(self, runtimeContext):
runtimeContext.keepprefix = "keep:"
- job_spec = self.arvados_job_spec(runtimeContext)
+ job_spec = self.arvados_job_spec(runtimeContext, self.git_info)
if runtimeContext.project_uuid:
job_spec["owner_uuid"] = runtimeContext.project_uuid