Merge branch 'master' of git.curoverse.com:arvados into 13429-cwl-runner-storage...

[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 a946452b6540301068cfce4ca9e651093ddc8753..4a6ccc0b2a331626f055d75eb1c54ac9d9a45b6a 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -37,7 +37,7 @@ import arvados.commands._util as arv_cmd
 
 from .arvcontainer import ArvadosContainer, RunnerContainer
 from .arvjob import ArvadosJob, RunnerJob, RunnerTemplate
-from. runner import Runner, upload_docker, upload_job_order, upload_workflow_deps, upload_dependencies
+from. runner import Runner, upload_docker, upload_job_order, upload_workflow_deps
 from .arvtool import ArvadosCommandTool
 from .arvworkflow import ArvadosWorkflow, upload_workflow
 from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver, CollectionCache
@@ -76,7 +76,6 @@ class ArvCwlRunner(object):
         self.workflow_eval_lock = threading.Condition(threading.RLock())
         self.final_output = None
         self.final_status = None
-        self.uploaded = {}
         self.num_retries = num_retries
         self.uuid = None
         self.stop_polling = threading.Event()
@@ -238,12 +237,6 @@ class ArvCwlRunner(object):
         finally:
             self.stop_polling.set()
 
-    def get_uploaded(self):
-        return self.uploaded.copy()
-
-    def add_uploaded(self, src, pair):
-        self.uploaded[src] = pair
-
     def add_intermediate_output(self, uuid):
         if uuid:
             self.intermediate_output_collections.append(uuid)
@@ -401,6 +394,9 @@ class ArvCwlRunner(object):
         if self.intermediate_output_ttl < 0:
             raise Exception("Invalid value %d for --intermediate-output-ttl, cannot be less than zero" % self.intermediate_output_ttl)
 
+        if kwargs.get("submit_request_uuid") and self.work_api != "containers":
+            raise Exception("--submit-request-uuid requires containers API, but using '{}' api".format(self.work_api))
+
         if not kwargs.get("name"):
             kwargs["name"] = self.name = tool.tool.get("label") or tool.metadata.get("label") or os.path.basename(tool.tool["id"])
 
@@ -709,6 +705,10 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         help="Docker image for workflow runner job, default arvados/jobs:%s" % __version__,
                         default=None)
 
+    parser.add_argument("--submit-request-uuid", type=str,
+                        default=None,
+                        help="Update and commit supplied container request instead of creating a new one (containers API only).")
+
     parser.add_argument("--name", type=str,
                         help="Name to use for workflow execution instance.",
                         default=None)