X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/1da448c49cb4ea4b8147e63f325102f793ca206c..08698803d8b324ba9a889a3aa41559d782bcc4bf:/sdk/cwl/arvados_cwl/arvcontainer.py?ds=sidebyside

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 19516d5b44..780ab89010 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -42,12 +42,22 @@ class ArvadosContainer(object):
             }
         }
 
+        dirs = set()
         for f in self.pathmapper.files():
-            _, p, _ = self.pathmapper.mapper(f)
-            mounts[p] = {
-                "kind": "collection",
-                "portable_data_hash": p[6:]
-            }
+            _, p, tp = self.pathmapper.mapper(f)
+            if tp == "Directory" and '/' not in p[6:]:
+                mounts[p] = {
+                    "kind": "collection",
+                    "portable_data_hash": p[6:]
+                }
+                dirs.add(p[6:])
+        for f in self.pathmapper.files():
+            _, p, tp = self.pathmapper.mapper(f)
+            if p[6:].split("/")[0] not in dirs:
+                mounts[p] = {
+                    "kind": "collection",
+                    "portable_data_hash": p[6:]
+                }
 
         if self.generatefiles["listing"]:
             raise UnsupportedRequirement("Generate files not supported")
@@ -90,7 +100,7 @@ class ArvadosContainer(object):
 
             self.arvrunner.processes[response["container_uuid"]] = self
 
-            logger.info("Container %s (%s) request state is %s", self.name, response["container_uuid"], response["state"])
+            logger.info("Container %s (%s) request state is %s", self.name, response["uuid"], response["state"])
 
             if response["state"] == "Final":
                 self.done(response)