Merge branch '10111-cr-provenance-graph'

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

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 5c697b37507ac81d583d8c3f721ef2b45d4c747f..9e76cf711ecaaf81c6e5e42131ea3d717da00c01 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -1,6 +1,7 @@
 import logging
 import json
 import os
+import urllib
 
 import ruamel.yaml as yaml
 
@@ -77,7 +78,7 @@ class ArvadosContainer(object):
                     "portable_data_hash": pdh
                 }
                 if len(sp) == 2:
-                    mounts[p]["path"] = sp[1]
+                    mounts[p]["path"] = urllib.unquote(sp[1])
 
         with Perf(metrics, "generatefiles %s" % self.name):
             if self.generatefiles["listing"]:
@@ -114,10 +115,14 @@ class ArvadosContainer(object):
             container_request["environment"].update(self.environment)
 
         if self.stdin:
-            raise UnsupportedRequirement("Stdin redirection currently not suppported")
+            sp = self.stdin[6:].split("/", 1)
+            mounts["stdin"] = {"kind": "collection",
+                                "portable_data_hash": sp[0],
+                                "path": sp[1]}
 
         if self.stderr:
-            raise UnsupportedRequirement("Stderr redirection currently not suppported")
+            mounts["stderr"] = {"kind": "file",
+                                "path": "%s/%s" % (self.outdir, self.stderr)}
 
         if self.stdout:
             mounts["stdout"] = {"kind": "file",