10576: Add retries to arvcontainer. Add command line options to documentation.

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

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index eb0afc19d82a899ccb5a3c7318abce28f7d12d12..dbbd83da2efd7d8f609dcdbfd90d10f414e6c1ac 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -37,7 +37,8 @@ class ArvadosContainer(object):
             "output_path": self.outdir,
             "cwd": self.outdir,
             "priority": 1,
-            "state": "Committed"
+            "state": "Committed",
+            "properties": {}
         }
         runtime_constraints = {}
         mounts = {
@@ -113,12 +114,20 @@ class ArvadosContainer(object):
         container_request["use_existing"] = kwargs.get("enable_reuse", True)
         container_request["scheduling_parameters"] = scheduling_parameters
 
+        if kwargs.get("runnerjob", "").startswith("arvwf:"):
+            wfuuid = kwargs["runnerjob"][6:kwargs["runnerjob"].index("#")]
+            wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(num_retries=self.arvrunner.num_retries)
+            if container_request["name"] == "main":
+                container_request["name"] = wfrecord["name"]
+            container_request["properties"]["template_uuid"] = wfuuid
+
         try:
             response = self.arvrunner.api.container_requests().create(
                 body=container_request
             ).execute(num_retries=self.arvrunner.num_retries)
 
-            self.arvrunner.processes[response["uuid"]] = self
+            self.uuid = response["uuid"]
+            self.arvrunner.processes[self.uuid] = self
 
             logger.info("Container request %s (%s) state is %s", self.name, response["uuid"], response["state"])
 
@@ -199,7 +208,8 @@ class RunnerContainer(Runner):
                 "vcpus": 1,
                 "ram": 1024*1024 * self.submit_runner_ram,
                 "API": True
-            }
+            },
+            "properties": {}
         }
 
         workflowcollection = workflowmapper.mapper(self.tool.tool["id"])[1]
@@ -213,14 +223,16 @@ class RunnerContainer(Runner):
                 }
         elif workflowcollection.startswith("arvwf:"):
             workflowpath = "/var/lib/cwl/workflow.json#main"
-            fetcher = CollectionFetcher({}, None,
-                                        api_client=self.arvrunner.api,
-                                        keep_client=self.arvrunner.keep_client)
-            wfobj = yaml.safe_load(fetcher.fetch_text(workflowcollection))
+            wfuuid = workflowcollection[6:workflowcollection.index("#")]
+            wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(num_retries=self.arvrunner.num_retries)
+            wfobj = yaml.safe_load(wfrecord["definition"])
+            if container_req["name"].startswith("arvwf:"):
+                container_req["name"] = wfrecord["name"]
             container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
                 "kind": "json",
                 "json": wfobj
             }
+            container_req["properties"]["template_uuid"] = wfuuid
 
         command = ["arvados-cwl-runner", "--local", "--api=containers"]
         if self.output_name:
@@ -251,7 +263,7 @@ class RunnerContainer(Runner):
         ).execute(num_retries=self.arvrunner.num_retries)
 
         self.uuid = response["uuid"]
-        self.arvrunner.processes[response["uuid"]] = self
+        self.arvrunner.processes[self.uuid] = self
 
         logger.info("Submitted container %s", response["uuid"])