[ARVADOS] updated: 8af4c785ee48083eac92a0bd1ccd0bf4c41a9410

[Git user]

Summary of changes:
 build/run-build-packages.sh         |   4 +-
 sdk/cwl/arvados_cwl/__init__.py     |   4 +-
 sdk/cwl/arvados_cwl/arvcontainer.py |  28 ++++++--
 sdk/cwl/arvados_cwl/arvjob.py       |  39 +++++++----
 sdk/cwl/arvados_cwl/arvtool.py      |   5 +-
 sdk/cwl/arvados_cwl/fsaccess.py     |  44 +++++++++++-
 sdk/cwl/arvados_cwl/pathmapper.py   | 135 +++++++++++++++++++++++++++++-------
 sdk/cwl/arvados_cwl/runner.py       |   7 +-
 sdk/cwl/setup.py                    |   7 +-
 sdk/go/crunchrunner/crunchrunner.go |  37 +++++++---
 sdk/python/arvados/commands/run.py  |   1 +
 11 files changed, 247 insertions(+), 64 deletions(-)

       via  8af4c785ee48083eac92a0bd1ccd0bf4c41a9410 (commit)
       via  af4c42cdaab573b9dc567f93680d68b1904b2528 (commit)
       via  331f76650627e742c0fc76d7c5fe37cdac847330 (commit)
       via  0422e3e8f46c7c54d7e33e2eedd805b05c76c7ce (commit)
       via  1da448c49cb4ea4b8147e63f325102f793ca206c (commit)
       via  27816b602e9da83a2565e6fe8f87f250555b1ba5 (commit)
       via  72ecf5e060b51c0b8c559329e713f8327a2e8c87 (commit)
       via  e34ddeba03a6a9b4a1f9913ff5871938e83ee1d2 (commit)
       via  a206b8127df92039645d5ad3f9e144380cc55613 (commit)
      from  28aa91f035205ede87ce62594ebacc36df50a84e (commit)

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commit 8af4c785ee48083eac92a0bd1ccd0bf4c41a9410
Merge: 28aa91f af4c42c
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed Jul 13 12:49:57 2016 -0400

    Merge branch '9570-cwl-v1.0' closes #9570


commit af4c42cdaab573b9dc567f93680d68b1904b2528
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed Jul 13 11:36:03 2016 -0400

    9570: Set docker_outdir consistently.

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 9f1c577..1959b5c 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -126,9 +126,11 @@ class ArvCwlRunner(object):
 
         if self.work_api == "containers":
             kwargs["outdir"] = "/var/spool/cwl"
+            kwargs["docker_outdir"] = "/var/spool/cwl"
             kwargs["tmpdir"] = "/tmp"
         elif self.work_api == "jobs":
             kwargs["outdir"] = "$(task.outdir)"
+            kwargs["docker_outdir"] = "$(task.outdir)"
             kwargs["tmpdir"] = "$(task.tmpdir)"
 
         runnerjob = None
@@ -169,7 +171,6 @@ class ArvCwlRunner(object):
                 self.uuid = kwargs.get("cwl_runner_job").get('uuid')
             jobiter = tool.job(job_order,
                                self.output_callback,
-                               docker_outdir="$(task.outdir)",
                                **kwargs)
 
         try:
diff --git a/sdk/cwl/arvados_cwl/arvtool.py b/sdk/cwl/arvados_cwl/arvtool.py
index 021365c..7107ba0 100644
--- a/sdk/cwl/arvados_cwl/arvtool.py
+++ b/sdk/cwl/arvados_cwl/arvtool.py
@@ -33,6 +33,8 @@ class ArvadosCommandTool(CommandLineTool):
     def job(self, joborder, output_callback, **kwargs):
         if self.work_api == "containers":
             kwargs["outdir"] = "/var/spool/cwl"
+            kwargs["docker_outdir"] = "/var/spool/cwl"
         elif self.work_api == "jobs":
             kwargs["outdir"] = "$(task.outdir)"
+            kwargs["docker_outdir"] = "$(task.outdir)"
         return super(ArvadosCommandTool, self).job(joborder, output_callback, **kwargs)

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