X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/e34ddeba03a6a9b4a1f9913ff5871938e83ee1d2..cae94f22b760c6c6899fc4d23db15d389535ff0a:/sdk/cwl/arvados_cwl/arvcontainer.py

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 5ad87d1ad0..413435db23 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -42,23 +42,36 @@ 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:
+        if self.generatefiles["listing"]:
             raise UnsupportedRequirement("Generate files not supported")
 
-        container_request["environment"] = {"TMPDIR": "/tmp"}
+        container_request["environment"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
         if self.environment:
             container_request["environment"].update(self.environment)
 
         if self.stdin:
             raise UnsupportedRequirement("Stdin redirection currently not suppported")
 
+        if self.stderr:
+            raise UnsupportedRequirement("Stderr redirection currently not suppported")
+
         if self.stdout:
             mounts["stdout"] = {"kind": "file",
                                 "path": "%s/%s" % (self.outdir, self.stdout)}
@@ -87,7 +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)