X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/5dc5645a3279e771796266eb336536ae0ac9cb86..d6a05be901e501bd10c00702fc8540dc1efba68a:/sdk/cwl/arvados_cwl/__init__.py

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 7bbb3b29e8..79bcee58ee 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -152,6 +152,10 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         help="When invoked with --submit --wait, always submit a runner to manage the workflow, even when only running a single CommandLineTool",
                         default=False)
 
+    parser.add_argument("--match-submitter-images", action="store_true",
+                        default=False, dest="match_local_docker",
+                        help="Where Arvados has more than one Docker image of the same name, use image from the Docker instance on the submitting node.")
+
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--submit-request-uuid",
                          default=None,
@@ -209,6 +213,14 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
     parser.add_argument("--http-timeout", type=int,
                         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("--enable-preemptible", dest="enable_preemptible", default=None, action="store_true", help="Use preemptible instances. Control individual steps with arv:UsePreemptible hint.")
+    exgroup.add_argument("--disable-preemptible", dest="enable_preemptible", default=None, action="store_false", help="Don't use preemptible instances.")
+
+    exgroup = parser.add_mutually_exclusive_group()
+    exgroup.add_argument("--copy-deps", dest="copy_deps", default=None, action="store_true", help="Copy dependencies into the destination project.")
+    exgroup.add_argument("--no-copy-deps", dest="copy_deps", default=None, action="store_false", help="Leave dependencies where they are.")
+
     parser.add_argument(
         "--skip-schemas",
         action="store_true",
@@ -249,14 +261,22 @@ def add_arv_hints():
         "http://arvados.org/cwl#IntermediateOutput",
         "http://arvados.org/cwl#ReuseRequirement",
         "http://arvados.org/cwl#ClusterTarget",
-        "http://arvados.org/cwl#OutputStorageClass"
+        "http://arvados.org/cwl#OutputStorageClass",
+        "http://arvados.org/cwl#ProcessProperties",
+        "http://commonwl.org/cwltool#CUDARequirement",
+        "http://arvados.org/cwl#UsePreemptible",
+        "http://arvados.org/cwl#OutputCollectionProperties",
     ])
 
 def exit_signal_handler(sigcode, frame):
     logger.error(str(u"Caught signal {}, exiting.").format(sigcode))
     sys.exit(-sigcode)
 
-def main(args, stdout, stderr, api_client=None, keep_client=None,
+def main(args=sys.argv[1:],
+         stdout=sys.stdout,
+         stderr=sys.stderr,
+         api_client=None,
+         keep_client=None,
          install_sig_handlers=True):
     parser = arg_parser()
 
@@ -300,7 +320,7 @@ def main(args, stdout, stderr, api_client=None, keep_client=None,
             api_client.users().current().execute()
         if keep_client is None:
             keep_client = arvados.keep.KeepClient(api_client=api_client, num_retries=4)
-        executor = ArvCwlExecutor(api_client, arvargs, keep_client=keep_client, num_retries=4)
+        executor = ArvCwlExecutor(api_client, arvargs, keep_client=keep_client, num_retries=4, stdout=stdout)
     except WorkflowException as e:
         logger.error(e, exc_info=(sys.exc_info()[1] if arvargs.debug else False))
         return 1
@@ -339,6 +359,10 @@ def main(args, stdout, stderr, api_client=None, keep_client=None,
         # unit tests.
         stdout = None
 
+    if arvargs.submit and arvargs.workflow.startswith("arvwf:"):
+        executor.loadingContext.do_validate = False
+        executor.fast_submit = True
+
     return cwltool.main.main(args=arvargs,
                              stdout=stdout,
                              stderr=stderr,
@@ -348,5 +372,5 @@ def main(args, stdout, stderr, api_client=None, keep_client=None,
                              logger_handler=arvados.log_handler,
                              custom_schema_callback=add_arv_hints,
                              loadingContext=executor.loadingContext,
-                             runtimeContext=executor.runtimeContext,
+                             runtimeContext=executor.toplevel_runtimeContext,
                              input_required=not (arvargs.create_workflow or arvargs.update_workflow))