From d182d19257f6cbe71fd75c29e1a81ba59a2aa79c Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Fri, 30 Sep 2016 17:35:52 -0400 Subject: [PATCH] 10165: Handle copying complete collection contents into subdirectory. --- sdk/cwl/arvados_cwl/__init__.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py index ef4f785529..5bdffd5048 100644 --- a/sdk/cwl/arvados_cwl/__init__.py +++ b/sdk/cwl/arvados_cwl/__init__.py @@ -188,7 +188,8 @@ class ArvCwlRunner(object): srccollections[srccollection] = arvados.collection.CollectionReader(srccollection) reader = srccollections[srccollection] try: - final.copy("/".join(sp[1:]), v.target, source_collection=reader, overwrite=False) + srcpath = "/".join(sp[1:]) if len(sp) > 1 else "." + final.copy(srcpath, v.target, source_collection=reader, overwrite=False) except IOError as e: logger.warn("While preparing output collection: %s", e) -- 2.39.5