[ARVADOS] updated: 09bd4574219cc4065ee356d0ce380cda20c9a883

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/arvcontainer.py | 4 ++--
 sdk/cwl/arvados_cwl/fsaccess.py     | 5 +++++
 services/crunch-run/crunchrun.go    | 5 +++--
 3 files changed, 10 insertions(+), 4 deletions(-)

       via  09bd4574219cc4065ee356d0ce380cda20c9a883 (commit)
       via  d42d65d2dabd31b403770c374ea5abdd194ccab4 (commit)
      from  5f82d0d9a0381605cdccfa1cfacaf670f139f47b (commit)

Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.


commit 09bd4574219cc4065ee356d0ce380cda20c9a883
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Mon Jun 13 16:42:37 2016 -0400

    8442: more import fixups, import workflow file correctly.

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 4c80896..414ce63 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -152,7 +152,7 @@ class RunnerContainer(Runner):
         workflowname = os.path.basename(self.tool.tool["id"])
         workflowpath = "/var/lib/cwl/workflow/%s" % workflowname
         workflowcollection = workflowmapper.mapper(self.tool.tool["id"])[1]
-        workflowcollection = workflowcollection[workflowcollection.index('/')]
+        workflowcollection = workflowcollection[:workflowcollection.index('/')]
         jobpath = "/var/lib/cwl/job/cwl.input.json"
 
         container_image = arv_docker_get_image(self.arvrunner.api,
@@ -170,7 +170,7 @@ class RunnerContainer(Runner):
             "state": "Committed",
             "container_image": container_image,
             "mounts": {
-                workflowpath: {
+                "/var/lib/cwl/workflow": {
                     "kind": "collection",
                     "portable_data_hash": "%s" % workflowcollection
                 },
diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index d48c93a..28b0fee 100644
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -1,6 +1,11 @@
 import fnmatch
+import os
+
 import cwltool.process
 
+import arvados.util
+import arvados.collection
+
 class CollectionFsAccess(cwltool.process.StdFsAccess):
     """Implement the cwltool FsAccess interface for Arvados Collections."""
 

commit d42d65d2dabd31b403770c374ea5abdd194ccab4
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Mon Jun 13 16:31:49 2016 -0400

    8442: Enable net when API is enabled.

diff --git a/services/crunch-run/crunchrun.go b/services/crunch-run/crunchrun.go
index f558345..d508ffb 100644
--- a/services/crunch-run/crunchrun.go
+++ b/services/crunch-run/crunchrun.go
@@ -482,10 +482,11 @@ func (runner *ContainerRunner) CreateContainer() error {
 			"ARVADOS_API_HOST="+os.Getenv("ARVADOS_API_HOST"),
 			"ARVADOS_API_HOST_INSECURE="+os.Getenv("ARVADOS_API_HOST_INSECURE"),
 		)
+		runner.ContainerConfig.NetworkDisabled = false
+	} else {
+		runner.ContainerConfig.NetworkDisabled = true
 	}
 
-	runner.ContainerConfig.NetworkDisabled = true
-
 	var err error
 	runner.ContainerID, err = runner.Docker.CreateContainer(&runner.ContainerConfig, "", nil)
 	if err != nil {

-----------------------------------------------------------------------


hooks/post-receive
--