- t = cwltool.main.load_tool(job_order_object, False, True, runner.arvMakeTool, True)
+ t = load_tool(job_order_object, runner.arvMakeTool)
+
+ args = argparse.Namespace()
+ args.project_uuid = arvados.current_job()["owner_uuid"]
+ args.enable_reuse = True
+ args.submit = False
+ args.debug = True
+ args.quiet = False
+ args.ignore_docker_for_reuse = False
+ args.basedir = os.getcwd()
+ args.cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]}
+ outputObj = runner.arvExecutor(t, job_order_object, **vars(args))
+
+ files = {}
+ def capture(fileobj):
+ path = fileobj["location"]
+ sp = path.split("/")
+ col = sp[0][5:]
+ if col not in files:
+ files[col] = set()
+ files[col].add("/".join(sp[1:]))
+ fileobj["location"] = path
+
+ adjustFileObjs(outputObj, capture)
+
+ final = arvados.collection.Collection()
+
+ for k,v in files.iteritems():
+ with arvados.collection.Collection(k) as c:
+ for f in c:
+ final.copy(f, f, c, True)
+
+ def makeRelative(fileobj):
+ fileobj["location"] = "/".join(fileobj["location"].split("/")[1:])