[ARVADOS] updated: 523dadebfbee9a73a21c3f78c7b4af329930d393

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/__init__.py        | 45 ++++++++++++------
 sdk/cwl/arvados_cwl/arv-cwl-schema.yml | 14 ++++++
 sdk/cwl/arvados_cwl/arvjob.py          |  3 ++
 sdk/cwl/arvados_cwl/arvworkflow.py     | 83 +++++++++++++++++++++++++++++++++-
 sdk/cwl/arvados_cwl/pathmapper.py      |  2 +-
 sdk/cwl/arvados_cwl/runner.py          |  2 +-
 sdk/cwl/setup.py                       |  1 +
 sdk/cwl/tests/test_job.py              | 68 ++++++++++++++++++++++++++--
 sdk/cwl/tests/wf/scatter2.cwl          | 56 +++++++++++++++++++++++
 sdk/cwl/tests/wf/scatter2_subwf.cwl    | 33 ++++++++++++++
 10 files changed, 287 insertions(+), 20 deletions(-)
 create mode 100644 sdk/cwl/arvados_cwl/arv-cwl-schema.yml
 create mode 100644 sdk/cwl/tests/wf/scatter2.cwl
 create mode 100644 sdk/cwl/tests/wf/scatter2_subwf.cwl

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commit 523dadebfbee9a73a21c3f78c7b4af329930d393
Merge: c2fdf5d 9bc524a
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Mon Sep 26 08:42:43 2016 -0400

    Merge branch '10081-cwl-run-same-job' closes #10081


commit 9bc524ae6d516f1be41cc8a7c6a76a96bbd9578c
Merge: 8b7d630 c858ed3
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Fri Sep 23 16:18:39 2016 -0400

    Merge branch 'master' into 10081-cwl-run-same-job
    
    Conflicts:
    	sdk/cwl/arvados_cwl/runner.py

diff --cc sdk/cwl/arvados_cwl/runner.py
index 2e52b63,bdd8077..cf2f1db
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@@ -87,8 -80,8 +80,8 @@@ def upload_dependencies(arvrunner, name
                             name=name)
  
      def setloc(p):
-         if not p["location"].startswith("keep:"):
-             p["location"] = mapper.mapper(p["location"]).resolved
 -        if not p["location"].startswith("_:"):
++        if not p["location"].startswith("_:") and not p["location"].startswith("keep:"):
+             p["location"] = mapper.mapper(p["location"]).target
      adjustFileObjs(workflowobj, setloc)
      adjustDirObjs(workflowobj, setloc)
  

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