if obj.get("location", "").startswith("_:"):
del obj["location"]
+def remove_redundant_fields(obj):
+ for field in ("path", "nameext", "nameroot", "dirname"):
+ if field in obj:
+ del obj[field]
+
def find_defaults(d, op):
if isinstance(d, list):
for i in d:
packed["http://schema.org/version"] = githash
-def upload_job_order(arvrunner, name, tool, job_order):
- """Upload local files referenced in the input object and return updated input
- object with 'location' updated to the proper keep references.
- """
-
- for t in tool.tool["inputs"]:
+def discover_secondary_files(inputs, job_order):
+ for t in inputs:
def setSecondary(fileobj):
if isinstance(fileobj, dict) and fileobj.get("class") == "File":
if "secondaryFiles" not in fileobj:
if shortname(t["id"]) in job_order and t.get("secondaryFiles"):
setSecondary(job_order[shortname(t["id"])])
+def upload_job_order(arvrunner, name, tool, job_order):
+ """Upload local files referenced in the input object and return updated input
+ object with 'location' updated to the proper keep references.
+ """
+
+ discover_secondary_files(tool.tool["inputs"], job_order)
+
jobmapper = upload_dependencies(arvrunner,
name,
tool.doc_loader,
self.tool = tool
self.job_order = job_order
self.running = False
+ if enable_reuse:
+ # If reuse is permitted by command line arguments but
+ # disabled by the workflow itself, disable it.
+ reuse_req, _ = get_feature(self.tool, "http://arvados.org/cwl#ReuseRequirement")
+ if reuse_req:
+ enable_reuse = reuse_req["enableReuse"]
self.enable_reuse = enable_reuse
self.uuid = None
self.final_output = None