12256: Fix anonymous directory default inputs with file literals

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/pathmapper.py b/sdk/cwl/arvados_cwl/pathmapper.py
index 998890a31c50acac0513479d0fad9675fd790647..6fedb120300b2bdb575a663614840c5ba765b7ec 100644 (file)
--- a/sdk/cwl/arvados_cwl/pathmapper.py
+++ b/sdk/cwl/arvados_cwl/pathmapper.py
@@ -107,6 +107,7 @@ class ArvPathMapper(PathMapper):
         elif obj["location"].startswith("_:") and "contents" in obj:
             with c.open(path + "/" + obj["basename"], "w") as f:
                 f.write(obj["contents"].encode("utf-8"))
+            remap.append((obj["location"], path + "/" + obj["basename"]))
         else:
             raise SourceLine(obj, "location", WorkflowException).makeError("Don't know what to do with '%s'" % obj["location"])