[ARVADOS] updated: cfa7968b0bf34ce7ba032492e18fe0e1ed77df9e

[Git user]

Summary of changes:
 README.md                                          |   2 +-
 build/run-tests.sh                                 |   4 +-
 sdk/cwl/arvados_cwl/__init__.py                    |  11 +-
 sdk/go/arvadostest/fixtures.go                     |   5 +-
 sdk/go/arvadostest/run_servers.go                  |  30 +-
 sdk/python/arvados/commands/keepdocker.py          |   7 +-
 .../crunch-dispatch-slurm/crunch-dispatch-slurm.go |  67 ++-
 .../crunch-dispatch-slurm_test.go                  |  86 +++-
 services/datamanager/datamanager_test.go           |  39 +-
 services/keep-balance/balance_run_test.go          |   2 +-
 services/keepstore/handlers.go                     |  18 +-
 services/keepstore/pull_worker.go                  |   5 +-
 services/keepstore/s3_volume.go                    | 487 ++++++++++++++++++---
 services/keepstore/s3_volume_test.go               | 217 ++++++++-
 services/keepstore/volume_generic_test.go          |  21 +-
 services/keepstore/volume_unix.go                  |  13 +-
 16 files changed, 874 insertions(+), 140 deletions(-)

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commit cfa7968b0bf34ce7ba032492e18fe0e1ed77df9e
Author: radhika <radhika at curoverse.com>
Date:   Thu Jul 28 13:36:26 2016 -0400

    9552: add compute-checksum flag to arvados-cwl-runner

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 4bff093..bb0979a 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -35,7 +35,7 @@ class ArvCwlRunner(object):
 
     """
 
-    def __init__(self, api_client, work_api=None):
+    def __init__(self, api_client, work_api=None, compute_checksum=False):
         self.api = api_client
         self.processes = {}
         self.lock = threading.Lock()
@@ -46,6 +46,7 @@ class ArvCwlRunner(object):
         self.num_retries = 4
         self.uuid = None
         self.work_api = work_api
+        self.compute_checksum = compute_checksum
 
         if self.work_api is None:
             # todo: autodetect API to use.
@@ -127,7 +128,7 @@ class ArvCwlRunner(object):
         kwargs["use_container"] = True
         kwargs["tmpdir_prefix"] = "tmp"
         kwargs["on_error"] = "continue"
-        kwargs["compute_checksum"] = False
+        kwargs["compute_checksum"] = self.compute_checksum
 
         if self.work_api == "containers":
             kwargs["outdir"] = "/var/spool/cwl"
@@ -291,6 +292,10 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         default=None, dest="work_api",
                         help="Select work submission API, one of 'jobs' or 'containers'.")
 
+    parser.add_argument("--compute-checksum", action="store_true", default=False,
+                        help="Compute checksum of contents while collecting outputs",
+                        dest="compute_checksum")
+
     parser.add_argument("workflow", type=str, nargs="?", default=None, help="The workflow to execute")
     parser.add_argument("job_order", nargs=argparse.REMAINDER, help="The input object to the workflow.")
 
@@ -308,7 +313,7 @@ def main(args, stdout, stderr, api_client=None):
     try:
         if api_client is None:
             api_client=arvados.api('v1', model=OrderedJsonModel())
-        runner = ArvCwlRunner(api_client, work_api=arvargs.work_api)
+        runner = ArvCwlRunner(api_client, work_api=arvargs.work_api, compute_checksum=arvargs.compute_checksum)
     except Exception as e:
         logger.error(e)
         return 1

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