[ARVADOS] updated: e68177bfa8de36bd54f705e16e5c4854eafb29a2

[Git user]

Summary of changes:
 build/run-build-packages.sh         |   4 +-
 crunch_scripts/cwl-runner           |  40 ++++---------
 sdk/cwl/arvados_cwl/__init__.py     |  92 +++++++++++++++++++++++++---
 sdk/cwl/arvados_cwl/arvcontainer.py |  11 +++-
 sdk/cwl/arvados_cwl/arvjob.py       |  14 ++++-
 sdk/cwl/arvados_cwl/fsaccess.py     |   6 +-
 sdk/cwl/arvados_cwl/pathmapper.py   |  28 +++++++--
 sdk/cwl/arvados_cwl/runner.py       |  10 +++-
 sdk/cwl/setup.py                    |   2 +-
 sdk/cwl/tests/test_job.py           | 116 +++++++++++++++++++-----------------
 sdk/cwl/tests/test_make_output.py   |  58 ++++++++++++++++++
 sdk/cwl/tests/test_submit.py        |  22 ++++---
 12 files changed, 287 insertions(+), 116 deletions(-)
 create mode 100644 sdk/cwl/tests/test_make_output.py

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commit e68177bfa8de36bd54f705e16e5c4854eafb29a2
Merge: a3562a6 d5cc112
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Thu Oct 6 11:34:34 2016 -0400

    Merge branch 'master' into 9307-cwl-use-tmp-output
    
    Conflicts:
    	sdk/cwl/tests/test_job.py

diff --cc sdk/cwl/tests/test_job.py
index db596ca,8317c8f..8d12aab
--- a/sdk/cwl/tests/test_job.py
+++ b/sdk/cwl/tests/test_job.py
@@@ -22,7 -22,8 +22,8 @@@ class TestJob(unittest.TestCase)
          runner = mock.MagicMock()
          runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
          runner.ignore_docker_for_reuse = False
+         runner.num_retries = 0
 -        document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
 +        document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
  
          tool = {
              "inputs": [],
@@@ -70,9 -71,9 +71,12 @@@
          runner = mock.MagicMock()
          runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
          runner.ignore_docker_for_reuse = False
+         runner.num_retries = 0
 -        document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
 +        arvados_cwl.add_arv_hints()
++
 +        document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
 +
+ 
          tool = {
              "inputs": [],
              "outputs": [],

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