Merge branch 'master' into 9514-only-delete-old-container-logs

[arvados.git] / sdk / cwl / arvados_cwl / pathmapper.py

diff --git a/sdk/cwl/arvados_cwl/pathmapper.py b/sdk/cwl/arvados_cwl/pathmapper.py
index 24c319cce5620dd9110f76932d45cb20967040bc..40a64ffd20b5a769421f297c8a29cf35cec1d8d3 100644 (file)
--- a/sdk/cwl/arvados_cwl/pathmapper.py
+++ b/sdk/cwl/arvados_cwl/pathmapper.py
@@ -52,13 +52,14 @@ class ArvPathMapper(PathMapper):
         elif srcobj["class"] == "Directory":
             if isinstance(src, basestring) and ArvPathMapper.pdh_dirpath.match(src):
                 self._pathmap[src] = MapperEnt(src, self.collection_pattern % src[5:], "Directory")
-            else:
-                for l in srcobj["listing"]:
-                    self.visit(l, uploadfiles)
+            for l in srcobj["listing"]:
+                self.visit(l, uploadfiles)
 
     def addentry(self, obj, c, path, subdirs):
         if obj["location"] in self._pathmap:
             src, srcpath = self.arvrunner.fs_access.get_collection(self._pathmap[obj["location"]].resolved)
+            if srcpath == "":
+                srcpath = "."
             c.copy(srcpath, path + "/" + obj["basename"], source_collection=src, overwrite=True)
             for l in obj.get("secondaryFiles", []):
                 self.addentry(l, c, path, subdirs)