[ARVADOS] updated: 0422e3e8f46c7c54d7e33e2eedd805b05c76c7ce

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/arvcontainer.py | 25 +++++++++++++++++++------
 sdk/cwl/arvados_cwl/pathmapper.py   |  4 ++++
 2 files changed, 23 insertions(+), 6 deletions(-)

       via  0422e3e8f46c7c54d7e33e2eedd805b05c76c7ce (commit)
       via  1da448c49cb4ea4b8147e63f325102f793ca206c (commit)
      from  27816b602e9da83a2565e6fe8f87f250555b1ba5 (commit)

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commit 0422e3e8f46c7c54d7e33e2eedd805b05c76c7ce
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed Jul 13 09:53:48 2016 -0400

    9570: Fix secondaryFile staging to ensure that all files are in the same
    collection.

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 19516d5..73ba8d5 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -42,12 +42,22 @@ 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["listing"]:
             raise UnsupportedRequirement("Generate files not supported")
diff --git a/sdk/cwl/arvados_cwl/pathmapper.py b/sdk/cwl/arvados_cwl/pathmapper.py
index 12f7cd7..0dc80fc 100644
--- a/sdk/cwl/arvados_cwl/pathmapper.py
+++ b/sdk/cwl/arvados_cwl/pathmapper.py
@@ -1,5 +1,6 @@
 import re
 import logging
+import uuid
 
 import arvados.commands.run
 import arvados.collection
@@ -123,6 +124,9 @@ class ArvPathMapper(PathMapper):
 
                 ab = self.file_pattern % (c.portable_data_hash(), srcobj["basename"])
                 self._pathmap[srcobj["location"]] = MapperEnt(ab, ab, "File")
+                if srcobj.get("secondaryFiles"):
+                    ab = self.collection_pattern % c.portable_data_hash()
+                    self._pathmap["_:" + unicode(uuid.uuid4())] = MapperEnt(ab, ab, "Directory")
                 for loc, sub in subdirs:
                     ab = self.file_pattern % (c.portable_data_hash(), sub[2:])
                     self._pathmap[loc] = MapperEnt(ab, ab, "Directory")

commit 1da448c49cb4ea4b8147e63f325102f793ca206c
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Jul 12 18:14:53 2016 -0400

    9570: Fix for Pathmapper API change.  Most tests pass or exit unsupported
    feature.

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 5ad87d1..19516d5 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -43,13 +43,13 @@ class ArvadosContainer(object):
         }
 
         for f in self.pathmapper.files():
-            _, p = self.pathmapper.mapper(f)
+            _, p, _ = self.pathmapper.mapper(f)
             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"}
@@ -59,6 +59,9 @@ class ArvadosContainer(object):
         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)}

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