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 20601243b1dee9272bc4cafa2326df0790bc6f53..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
 
@@ -53,7 +54,7 @@ class ArvadosContainer(object):
 
         dirs = set()
         for f in self.pathmapper.files():
-            pdh, p, tp = self.pathmapper.mapper(f)
+            pdh, p, tp, stg = self.pathmapper.mapper(f)
             if tp == "Directory" and '/' not in pdh:
                 mounts[p] = {
                     "kind": "collection",
@@ -62,15 +63,22 @@ class ArvadosContainer(object):
                 dirs.add(pdh)
 
         for f in self.pathmapper.files():
-            res, p, tp = self.pathmapper.mapper(f)
-            pdh, path = res[5:].split("/", 1)
+            res, p, tp, stg = self.pathmapper.mapper(f)
+            if res.startswith("keep:"):
+                res = res[5:]
+            elif res.startswith("/keep/"):
+                res = res[6:]
+            else:
+                continue
+            sp = res.split("/", 1)
+            pdh = sp[0]
             if pdh not in dirs:
                 mounts[p] = {
                     "kind": "collection",
                     "portable_data_hash": pdh
                 }
-                if path:
-                    mounts[p]["path"] = path
+                if len(sp) == 2:
+                    mounts[p]["path"] = urllib.unquote(sp[1])
 
         with Perf(metrics, "generatefiles %s" % self.name):
             if self.generatefiles["listing"]:
@@ -107,10 +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",