[ARVADOS] updated: 9f53e085c98249ba79d85ba59e6f1ca624fede10

[Git user]

Summary of changes:
 .../methods/container_requests.html.textile.liquid |  2 +-
 sdk/cwl/arvados_cwl/__init__.py                    | 67 +++++++++++++---------
 sdk/cwl/arvados_cwl/arvcontainer.py                |  4 +-
 sdk/cwl/arvados_cwl/arvjob.py                      | 15 +++--
 sdk/cwl/arvados_cwl/runner.py                      |  4 +-
 5 files changed, 56 insertions(+), 36 deletions(-)

       via  9f53e085c98249ba79d85ba59e6f1ca624fede10 (commit)
       via  a07c8bfac95524f3074d11cda0d6689b5e7bf9cc (commit)
       via  20d3523229805ee800ec11bf4ab6e41c4e18eea6 (commit)
      from  c40265a873d73f03a9ca077f18fe305d883fb4a5 (commit)

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not appeared on any other notification email; so we list those
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commit 9f53e085c98249ba79d85ba59e6f1ca624fede10
Merge: c40265a a07c8bf
Author: radhika <radhika at curoverse.com>
Date:   Thu Nov 17 14:21:16 2016 -0500

    Merge branch 'master' into 10293-cwl-cr-output
    
    Conflicts:
    	sdk/cwl/arvados_cwl/__init__.py
    	sdk/cwl/arvados_cwl/arvcontainer.py

diff --cc doc/api/methods/container_requests.html.textile.liquid
index 1d7a244,304226d..05a8cf5
--- a/doc/api/methods/container_requests.html.textile.liquid
+++ b/doc/api/methods/container_requests.html.textile.liquid
@@@ -43,11 -40,9 +43,11 @@@ table(table table-bordered table-conden
  |cwd|string|Initial working directory, given as an absolute path (in the container) or a path relative to the WORKDIR given in the image's Dockerfile.|Required.|
  |command|array of strings|Command to execute in the container.|Required. e.g., @["echo","hello"]@|
  |output_path|string|Path to a directory or file inside the container that should be preserved as container's output when it finishes. This path must be, or be inside, one of the mount targets. For best performance, point output_path to a writable collection mount.|Required.|
--|priority|integer|Higher value means spend more resources on this container_request, i.e., go ahead of other queued containers, bring up more nodes etc.|Priority 0 means a container should not be run on behalf of this request. Clients are expected to submit container requests with zero priority in order to prevew the container that will be used to satisfy it. Priority can be null if and only if state!="Committed".|
++|priority|integer|Higher value means spend more resources on this container_request, i.e., go ahead of other queued containers, bring up more nodes etc.|Priority 0 means a container should not be run on behalf of this request. Clients are expected to submit container requests with zero priority in order to preview the container that will be used to satisfy it. Priority can be null if and only if state!="Committed".|
  |expires_at|datetime|After this time, priority is considered to be zero.|Not yet implemented.|
  |use_existing|boolean|If possible, use an existing (non-failed) container to satisfy the request instead of creating a new one.|Default is true|
 +|log_uuid|string|Log collection containing log messages provided by the scheduler and crunch processes.|Null if the container has not yet completed.|
 +|output_uuid|string|Output collection created when the container finished successfully.|Null if the container has failed or not yet completed.|
  |filters|string|Additional constraints for satisfying the container_request, given in the same form as the filters parameter accepted by the container_requests.list API.|
  
  h2(#mount_types). {% include 'mount_types' %}
diff --cc sdk/cwl/arvados_cwl/arvcontainer.py
index 178aeef,1fda412..b127f68
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@@ -145,7 -146,24 +145,9 @@@ class ArvadosContainer(object)
              else:
                  processStatus = "permanentFail"
  
-             outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
 -            try:
 -                outputs = {}
 -                if record["output"]:
 -                    outputs = done.done(self, record, "/tmp", self.outdir, "/keep")
 -            except WorkflowException as e:
 -                logger.error("Error while collecting output for container %s:\n%s", self.name, e, exc_info=(e if self.arvrunner.debug else False))
 -                processStatus = "permanentFail"
 -            except Exception as e:
 -                logger.exception("Got unknown exception while collecting output for container %s:", self.name)
 -                processStatus = "permanentFail"
 -
 -            # Note: Currently, on error output_callback is expecting an empty dict,
 -            # anything else will fail.
 -            if not isinstance(outputs, dict):
 -                logger.error("Unexpected output type %s '%s'", type(outputs), outputs)
 -                outputs = {}
 -                processStatus = "permanentFail"
 -
++            outputs = {}
++            if container["output"]:
++                outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
              self.output_callback(outputs, processStatus)
          finally:
              del self.arvrunner.processes[record["uuid"]]

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