Add timeout for the python api + A.C.R.

Arvados-DCO-1.1-Signed-off-by: Thomas Hickman <th10@sanger.ac.uk>

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 5b29ae517e8b15c33781cd70247c36d2ae831b94..2f11f996e79921c4e23debe66f0e5cb1aede4eba 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -512,7 +512,7 @@ class ArvCwlRunner(object):
             runnerjob.run(**submitargs)
             return (runnerjob.uuid, "success")
 
-        self.poll_api = arvados.api('v1')
+        self.poll_api = arvados.api('v1', timeout=kwargs["http-timeout"])
         self.polling_thread = threading.Thread(target=self.poll_states)
         self.polling_thread.start()
 
@@ -737,6 +737,9 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
     parser.add_argument("--thread-count", type=int,
                         default=4, help="Number of threads to use for job submit and output collection.")
 
+    parser.add_argument("--http-timeout", type=int,
+                        default=5*60, help="Http timeout. Default is 5 minutes.")
+
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--trash-intermediate", action="store_true",
                         default=False, dest="trash_intermediate",
@@ -801,7 +804,9 @@ def main(args, stdout, stderr, api_client=None, keep_client=None,
 
     try:
         if api_client is None:
-            api_client = arvados.safeapi.ThreadSafeApiCache(api_params={"model": OrderedJsonModel()}, keep_params={"num_retries": 4})
+            api_client = arvados.safeapi.ThreadSafeApiCache(
+                api_params={"model": OrderedJsonModel(), "timeout": arvargs.http_timeout},
+                keep_params={"num_retries": 4})
             keep_client = api_client.keep
         if keep_client is None:
             keep_client = arvados.keep.KeepClient(api_client=api_client, num_retries=4)

diff --git a/sdk/python/arvados/api.py b/sdk/python/arvados/api.py
index 4611a1aadf80043eb9afdeeaff727b27a09eecbc..7e9ad1ee81ad401feae2d0205e4516accbdbd96d 100644 (file)
--- a/sdk/python/arvados/api.py
+++ b/sdk/python/arvados/api.py
@@ -149,7 +149,7 @@ def http_cache(data_type):
     return cache.SafeHTTPCache(path, max_age=60*60*24*2)
 
 def api(version=None, cache=True, host=None, token=None, insecure=False,
-        request_id=None, **kwargs):
+        request_id=None, timeout=5*60, **kwargs):
     """Return an apiclient Resources object for an Arvados instance.
 
     :version:
@@ -169,6 +169,9 @@ def api(version=None, cache=True, host=None, token=None, insecure=False,
     :insecure:
       If True, ignore SSL certificate validation errors.
 
+    :timeout:
+      A timeout value for http requests.
+
     :request_id:
       Default X-Request-Id header value for outgoing requests that
       don't already provide one. If None or omitted, generate a random
@@ -221,6 +224,9 @@ def api(version=None, cache=True, host=None, token=None, insecure=False,
             http_kwargs['disable_ssl_certificate_validation'] = True
         kwargs['http'] = httplib2.Http(**http_kwargs)
 
+    if kwargs['http'].timeout is None:
+        kwargs['http'].timeout = timeout
+
     kwargs['http'] = _patch_http_request(kwargs['http'], token)
 
     svc = apiclient_discovery.build('arvados', version, cache_discovery=False, **kwargs)