+def upload_instance(arvrunner, name, tool, job_order):
+ upload_docker(arvrunner, tool)
+
+ for t in tool.tool["inputs"]:
+ def setSecondary(fileobj):
+ if "__norecurse" in fileobj:
+ del fileobj["__norecurse"]
+ return
+ if "secondaryFiles" not in fileobj:
+ fileobj["secondaryFiles"] = [{"location": substitute(fileobj["location"], sf), "class": "File", "__norecurse": True} for sf in t["secondaryFiles"]]
+
+ if shortname(t["id"]) in job_order and t.get("secondaryFiles"):
+ adjustFileObjs(job_order, setSecondary)
+
+ workflowmapper = upload_dependencies(arvrunner,
+ name,
+ tool.doc_loader,
+ tool.tool,
+ tool.tool["id"],
+ True)
+ jobmapper = upload_dependencies(arvrunner,
+ os.path.basename(job_order.get("id", "#")),
+ tool.doc_loader,
+ job_order,
+ job_order.get("id", "#"),
+ False)
+
+ if "id" in job_order:
+ del job_order["id"]
+
+ return workflowmapper
+
+def arvados_jobs_image(arvrunner):
+ img = "arvados/jobs:"+__version__
+ try:
+ arv_docker_get_image(arvrunner.api, {"dockerPull": img}, True, arvrunner.project_uuid)
+ except Exception as e:
+ raise Exception("Docker image %s is not available\n%s" % (img, e) )
+ return img