fs_access=CollectionFsAccess("", collection_cache=self.collection_cache),
num_retries=self.num_retries,
overrides=kwargs.get("override_tools"))
+ kwargs["resolver"] = partial(collectionResolver, self.api, num_retries=self.num_retries)
if "class" in toolpath_object and toolpath_object["class"] == "CommandLineTool":
return ArvadosCommandTool(self, toolpath_object, **kwargs)
elif "class" in toolpath_object and toolpath_object["class"] == "Workflow":
self.check_features(v)
elif isinstance(obj, list):
for i,v in enumerate(obj):
- with SourceLine(obj, i, UnsupportedRequirement):
+ with SourceLine(obj, i, UnsupportedRequirement, logger.isEnabledFor(logging.DEBUG)):
self.check_features(v)
def make_output_collection(self, name, tagsString, outputObj):
def rewrite(fileobj):
fileobj["location"] = generatemapper.mapper(fileobj["location"]).target
- for k in ("basename", "listing", "contents"):
+ for k in ("basename", "listing", "contents", "nameext", "nameroot", "dirname"):
if k in fileobj:
del fileobj[k]