19688: Trying a fast path submit for registered workflows

[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 ec9c52c59aac69a5881cc25ccf0a4267e3e4e7ab..57ab7367a34bb2a176454ed42a9f98aaae71f166 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -37,6 +37,9 @@ from ._version import __version__
 logger = logging.getLogger('arvados.cwl-runner')
 metrics = logging.getLogger('arvados.cwl-runner.metrics')
 
+def cleanup_name_for_collection(name):
+    return name.replace("/", " ")
+
 class ArvadosContainer(JobBase):
     """Submit and manage a Crunch container request for executing a CWL CommandLineTool."""
 
@@ -88,6 +91,8 @@ class ArvadosContainer(JobBase):
         container_request["state"] = "Committed"
         container_request.setdefault("properties", {})
 
+        container_request["properties"]["cwl_input"] = self.joborder
+
         runtime_constraints = {}
 
         if runtimeContext.project_uuid:
@@ -320,7 +325,7 @@ class ArvadosContainer(JobBase):
         if runtimeContext.submit_runner_cluster:
             extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster
 
-        container_request["output_name"] = "Output from step %s" % (self.name)
+        container_request["output_name"] = cleanup_name_for_collection("Output from step %s" % (self.name))
         container_request["output_ttl"] = self.output_ttl
         container_request["mounts"] = mounts
         container_request["secret_mounts"] = secret_mounts
@@ -349,8 +354,8 @@ class ArvadosContainer(JobBase):
                 for pr in output_properties_req["outputProperties"]:
                     container_request["output_properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"])
             else:
-                logger.warning("%s API server is too old to support setting properties on output collections.",
-                               self.arvrunner.label(self))
+                logger.warning("%s API revision is %s, revision %s is required to support setting properties on output collections.",
+                               self.arvrunner.label(self), self.arvrunner.api._rootDesc["revision"], "20220510")
 
         if runtimeContext.runnerjob.startswith("arvwf:"):
             wfuuid = runtimeContext.runnerjob[6:runtimeContext.runnerjob.index("#")]
@@ -434,6 +439,13 @@ class ArvadosContainer(JobBase):
 
             if container["output"]:
                 outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
+
+            properties = record["properties"].copy()
+            properties["cwl_output"] = outputs
+            self.arvrunner.api.container_requests().update(
+                uuid=self.uuid,
+                body={"container_request": {"properties": properties}}
+            ).execute(num_retries=self.arvrunner.num_retries)
         except WorkflowException as e:
             # Only include a stack trace if in debug mode.
             # A stack trace may obfuscate more useful output about the workflow.
@@ -450,7 +462,7 @@ class ArvadosContainer(JobBase):
 class RunnerContainer(Runner):
     """Submit and manage a container that runs arvados-cwl-runner."""
 
-    def arvados_job_spec(self, runtimeContext):
+    def arvados_job_spec(self, runtimeContext, git_info):
         """Create an Arvados container request for this workflow.
 
         The returned dict can be used to create a container passed as
@@ -511,15 +523,24 @@ class RunnerContainer(Runner):
                 "kind": "collection",
                 "portable_data_hash": "%s" % workflowcollection
             }
+        elif self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
+            workflowpath = "/var/lib/cwl/workflow.json#main"
+            record = self.arvrunner.api.workflows().get(uuid=self.embedded_tool.tool["id"][6:33]).execute(num_retries=self.arvrunner.num_retries)
+            packed = yaml.safe_load(record["definition"])
+            container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
+                "kind": "json",
+                "content": packed
+            }
+            container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
         else:
-            packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map, runtimeContext)
+            packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map, runtimeContext, git_info)
             workflowpath = "/var/lib/cwl/workflow.json#main"
             container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
                 "kind": "json",
                 "content": packed
             }
-            if self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
-                container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
+
+        container_req["properties"].update({k.replace("http://arvados.org/cwl#", "arv:"): v for k, v in git_info.items()})
 
         properties_req, _ = self.embedded_tool.get_requirement("http://arvados.org/cwl#ProcessProperties")
         if properties_req:
@@ -592,7 +613,7 @@ class RunnerContainer(Runner):
 
     def run(self, runtimeContext):
         runtimeContext.keepprefix = "keep:"
-        job_spec = self.arvados_job_spec(runtimeContext)
+        job_spec = self.arvados_job_spec(runtimeContext, self.git_info)
         if runtimeContext.project_uuid:
             job_spec["owner_uuid"] = runtimeContext.project_uuid