14018: Setting process properties WIP

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

diff --git a/sdk/cwl/arvados_cwl/arv-cwl-schema-v1.2.yml b/sdk/cwl/arvados_cwl/arv-cwl-schema-v1.2.yml
index dd5919fc88033b44eefdcb851711ac1c447bc8c6..17c37cf5c97414dbfc7b6bf692c51861dcf67fe0 100644 (file)
--- a/sdk/cwl/arvados_cwl/arv-cwl-schema-v1.2.yml
+++ b/sdk/cwl/arvados_cwl/arv-cwl-schema-v1.2.yml
@@ -239,3 +239,38 @@ $graph:
         - type: array
           items: string
       doc: One or more storages classes
+
+
+- type: record
+  name: PropertyDef
+  doc: |
+    Define a property that will be set on the submitted container
+    request associated with this workflow or step.
+  fields:
+    - name: propertyName
+      type: string
+      doc: The property key
+    - name: propertyValue
+      type: [cwl:Expression, Any]
+      doc: The property value
+
+
+- name: ProcessProperties
+  type: record
+  extends: cwl:ProcessRequirement
+  inVocab: false
+  doc: |
+    Specify metadata properties that will be set on the submitted
+    container request associated with this workflow or step.
+  fields:
+    class:
+      type: string
+      doc: "Always 'arv:ProcessProperties"
+      jsonldPredicate:
+        _id: "@type"
+        _type: "@vocab"
+    processProperties:
+      type: PropertyDef[]
+      jsonldPredicate:
+        mapSubject: propertyName
+        mapPredicate: propertyValue

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index c9170c51b732deee8f5a8bc383746c527ae5def7..c6e4577d03bcd8d36af869d8b6ec63cc2531bc47 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -67,15 +67,21 @@ class ArvadosContainer(JobBase):
 
         runtimeContext = self.job_runtime
 
-        container_request = {
-            "command": self.command_line,
-            "name": self.name,
-            "output_path": self.outdir,
-            "cwd": self.outdir,
-            "priority": runtimeContext.priority,
-            "state": "Committed",
-            "properties": {},
-        }
+        if runtimeContext.submit_request_uuid:
+            container_request = self.arvrunner.api.container_requests().get(
+                uuid=runtimeContext.submit_request_uuid
+            ).execute(num_retries=self.arvrunner.num_retries)
+        else:
+            container_request = {}
+
+        container_request["command"] = self.command_line
+        container_request["name"] = self.name
+        container_request["output_path"] = self.outdir
+        container_request["cwd"] = self.outdir
+        container_request["priority"] = runtimeContext.priority
+        container_request["state"] = "Committed"
+        container_request.setdefault("properties", {})
+
         runtime_constraints = {}
 
         if runtimeContext.project_uuid:
@@ -303,6 +309,11 @@ class ArvadosContainer(JobBase):
                 enable_reuse = reuse_req["enableReuse"]
         container_request["use_existing"] = enable_reuse
 
+        properties_req, _ = self.get_requirement("http://arvados.org/cwl#ProcessProperties")
+        if properties_req:
+            for pr in properties_req["processProperties"]:
+                container_request["properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"])
+
         if runtimeContext.runnerjob.startswith("arvwf:"):
             wfuuid = runtimeContext.runnerjob[6:runtimeContext.runnerjob.index("#")]
             wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(num_retries=self.arvrunner.num_retries)
@@ -468,6 +479,11 @@ class RunnerContainer(Runner):
             if self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
                 container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
 
+        properties_req, _ = self.embedded_tool.get_requirement("http://arvados.org/cwl#ProcessProperties")
+        if properties_req:
+            builder = make_builder(self.job_order, self.embedded_tool.hints, self.embedded_tool.requirements, runtimeContext, self.embedded_tool.metadata)
+            for pr in properties_req["processProperties"]:
+                container_request["properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"])
 
         # --local means execute the workflow instead of submitting a container request
         # --api=containers means use the containers API