Merge branch 'wtsi/13809-root_url-protocol-port-configuration'

[arvados.git] / sdk / cwl / arvados_cwl / __init__.py

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index a7e698b6dc346c1a6041763ccf8cc7a14d97d687..da24dc48465426ced81d1d37311b271bf45132a4 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -135,6 +135,21 @@ class ArvCwlRunner(object):
             else:
                 raise Exception("Unsupported API '%s', expected one of %s" % (work_api, expected_api))
 
+        if self.work_api == "jobs":
+            logger.warn("""
+*******************************
+Using the deprecated 'jobs' API.
+
+To get rid of this warning:
+
+Users: read about migrating at
+http://doc.arvados.org/user/cwl/cwl-style.html#migrate
+and use the option --api=containers
+
+Admins: configure the cluster to disable the 'jobs' API as described at:
+http://doc.arvados.org/install/install-api-server.html#disable_api_methods
+*******************************""")
+
         self.loadingContext = ArvLoadingContext(vars(arvargs))
         self.loadingContext.fetcher_constructor = self.fetcher_constructor
         self.loadingContext.resolver = partial(collectionResolver, self.api, num_retries=self.num_retries)
@@ -463,6 +478,7 @@ class ArvCwlRunner(object):
         runtimeContext = runtimeContext.copy()
         runtimeContext.use_container = True
         runtimeContext.tmpdir_prefix = "tmp"
+        runtimeContext.work_api = self.work_api
 
         if self.work_api == "containers":
             if self.ignore_docker_for_reuse:
@@ -527,7 +543,7 @@ 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()
 
@@ -713,7 +729,7 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
 
     parser.add_argument("--submit-runner-ram", type=int,
                         help="RAM (in MiB) required for the workflow runner job (default 1024)",
-                        default=1024)
+                        default=None)
 
     parser.add_argument("--submit-runner-image", type=str,
                         help="Docker image for workflow runner job, default arvados/jobs:%s" % __version__,
@@ -756,6 +772,9 @@ 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, dest="http_timeout", 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",
@@ -828,8 +847,12 @@ 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
+            # Make an API object now so errors are reported early.
+            api_client.users().current().execute()
         if keep_client is None:
             keep_client = arvados.keep.KeepClient(api_client=api_client, num_retries=4)
         runner = ArvCwlRunner(api_client, arvargs, keep_client=keep_client, num_retries=4)