with Perf(metrics, "setloc"):
visit_class(workflowobj, ("File", "Directory"), partial(setloc, mapper))
+def apply_merged_map(merged_map, workflowobj):
+ def visit(v, cur_id):
+ if isinstance(v, dict):
+ if v.get("class") in ("CommandLineTool", "Workflow", "ExpressionTool"):
+ if "id" in v:
+ cur_id = v["id"]
+ if "path" in v and "location" not in v:
+ v["location"] = v["path"]
+ del v["path"]
+ if "location" in v and cur_id in merged_map:
+ if v["location"] in merged_map[cur_id].resolved:
+ v["location"] = merged_map[cur_id].resolved[v["location"]]
+ if v["location"] in merged_map[cur_id].secondaryFiles:
+ v["secondaryFiles"] = merged_map[cur_id].secondaryFiles[v["location"]]
+ #if v.get("class") == "DockerRequirement":
+ # v["http://arvados.org/cwl#dockerCollectionPDH"] = arvados_cwl.arvdocker.arv_docker_get_image(arvrunner.api, v, True,
+ # runtimeContext)
+ for l in v:
+ visit(v[l], cur_id)
+ if isinstance(v, list):
+ for l in v:
+ visit(l, cur_id)
+ visit(workflowobj, None)
+
+def update_from_merged_map(tool, merged_map):
+ tool.visit(partial(apply_merged_map, merged_map))
+
def upload_job_order(arvrunner, name, tool, job_order, runtimeContext):
"""Upload local files referenced in the input object and return updated input
object with 'location' updated to the proper keep references.
update_from_mapper(job_order, jobmapper)
- #print(json.dumps(job_order, indent=2))
-
- return job_order
+ return job_order, jobmapper
FileUpdates = namedtuple("FileUpdates", ["resolved", "secondaryFiles"])
toolmap = {}
for k,v in pm.items():
toolmap[k] = v.resolved
+
merged_map[deptool["id"]] = FileUpdates(toolmap, discovered_secondaryfiles)
return merged_map