[ARVADOS] updated: 1.2.0-24-g490f5378e

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/__init__.py | 5 +++--
 sdk/cwl/arvados_cwl/context.py  | 1 +
 2 files changed, 4 insertions(+), 2 deletions(-)

       via  490f5378e5e902fcf9735fc5520a515c989f350a (commit)
      from  64e905e02fae8d63112be8a83b8f9f5f158fb2a2 (commit)

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commit 490f5378e5e902fcf9735fc5520a515c989f350a
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Wed Sep 5 17:37:57 2018 -0400

    Add http_timeout to runtimeContext refs #13542
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index da24dc484..940a488ae 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -543,7 +543,7 @@ http://doc.arvados.org/install/install-api-server.html#disable_api_methods
             runnerjob.run(submitargs)
             return (runnerjob.uuid, "success")
 
-        self.poll_api = arvados.api('v1', timeout=kwargs["http_timeout"])
+        self.poll_api = arvados.api('v1', timeout=runtimeContext.http_timeout)
         self.polling_thread = threading.Thread(target=self.poll_states)
         self.polling_thread.start()
 
@@ -773,7 +773,7 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         default=4, help="Number of threads to use for job submit and output collection.")
 
     parser.add_argument("--http-timeout", type=int,
-                        default=5*60, dest="http_timeout", help="Http timeout. Default is 5 minutes.")
+                        default=5*60, dest="http_timeout", help="API request timeout in seconds. Default is 300 seconds (5 minutes).")
 
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--trash-intermediate", action="store_true",
@@ -887,6 +887,7 @@ def main(args, stdout, stderr, api_client=None, keep_client=None,
     runtimeContext = ArvRuntimeContext(vars(arvargs))
     runtimeContext.make_fs_access = partial(CollectionFsAccess,
                              collection_cache=runner.collection_cache)
+    runtimeContext.http_timeout = arvargs.http_timeout
 
     return cwltool.main.main(args=arvargs,
                              stdout=stdout,
diff --git a/sdk/cwl/arvados_cwl/context.py b/sdk/cwl/arvados_cwl/context.py
index 81e256ed5..48a3edec5 100644
--- a/sdk/cwl/arvados_cwl/context.py
+++ b/sdk/cwl/arvados_cwl/context.py
@@ -29,5 +29,6 @@ class ArvRuntimeContext(RuntimeContext):
         self.cwl_runner_job = None
         self.storage_classes = "default"
         self.current_container = None
+        self.http_timeout = 300
 
         super(ArvRuntimeContext, self).__init__(kwargs)

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