import ruamel.yaml as yaml
-from .runner import upload_docker, upload_dependencies, del_listing
+from .runner import upload_docker, upload_dependencies, trim_listing
from .arvtool import ArvadosCommandTool
logger = logging.getLogger('arvados.cwl-runner')
packed = pack(document_loader, workflowobj, uri, tool.metadata)
- adjustDirObjs(job_order, del_listing)
+ adjustDirObjs(job_order, trim_listing)
main = [p for p in packed["$graph"] if p["id"] == "#main"][0]
for inp in main["inputs"]:
cwltool.draft2tool.ACCEPTLIST_RE = re.compile(r"^[a-zA-Z0-9._+-]+$")
-def del_listing(obj):
+def trim_listing(obj):
+ """Remove 'listing' field from Directory objects that are keep references.
+
+ When Directory objects represent Keep references, it redundant and
+ potentially very expensive to pass fully enumerated Directory objects
+ between instances of cwl-runner (e.g. a submitting a job, or using the
+ RunInSingleContainer feature), so delete the 'listing' field when it is
+ safe to do so.
+ """
+
if obj.get("location", "").startswith("keep:") and "listing" in obj:
del obj["listing"]
if obj.get("location", "").startswith("_:"):
self.job_order.get("id", "#"),
False)
- adjustDirObjs(self.job_order, del_listing)
+ adjustDirObjs(self.job_order, trim_listing)
if "id" in self.job_order:
del self.job_order["id"]