Bug fix for nested inputBinding valueFrom. Also encode CreateFileRequirement

output as utf-8.

Author: Peter Amstutz

cwltool/builder.py

@@ -57,7 +57,7 @@ def bind_input(self, schema, datum, lead_pos=[], tail_pos=[]):
             else:
                 binding["position"] = aslist(lead_pos) + [0] + aslist(tail_pos)
 
-            if "valueFrom" in binding:
+            if "valueFrom" in binding and "do_eval" not in binding:
                 binding["do_eval"] = binding["valueFrom"]
             binding["valueFrom"] = datum
 

cwltool/job.py

@@ -172,7 +172,7 @@ def run(self, dry_run=False, pull_image=True, rm_container=True,
                         os.symlink(src, dst)
                 elif isinstance(entry, (str, unicode)):
                     with open(os.path.join(self.outdir, t), "w") as fout:
-                        fout.write(entry)
+                        fout.write(entry.encode("utf-8"))
                 else:
                     raise Exception("Unhandled type %s", type(entry))