8558: add min_cores_per_node and min_ram_mb_per_node to runtime_constraints from...

[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 0b90c78f31701fabd4bd7fe6d779b160f39eafc5..ca807951bd8634db11fcc70c95f1899952e62b14 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -152,6 +152,19 @@ class ArvadosJob(object):
         if docker_req and kwargs.get("use_container") is not False:
             runtime_constraints["docker_image"] = arv_docker_get_image(self.arvrunner.api, docker_req, pull_image)
 
+        resources = self.builder.resources
+        if resources is not None:
+            if "coresMin" in resources.keys():
+                try:
+                    runtime_constraints["min_cores_per_node"] = int(resources["coresMin"])
+                except:
+                    runtime_constraints["min_cores_per_node"] = None
+            if "ramMin" in resources.keys():
+                try:
+                    runtime_constraints["min_ram_mb_per_node"] = int(resources["ramMin"])
+                except:
+                    runtime_constraints["min_ram_mb_per_node"] = None
+
         try:
             response = self.arvrunner.api.jobs().create(body={
                 "script": "crunchrunner",
@@ -218,6 +231,7 @@ class ArvadosJob(object):
                             break
 
                     self.builder.outdir = outdir
+                    self.builder.pathmapper.keepdir = keepdir
                     outputs = self.collect_outputs("keep:" + record["output"])
             except Exception as e:
                 logger.exception("Got exception while collecting job outputs:")
@@ -261,6 +275,15 @@ class ArvPathMapper(cwltool.pathmapper.PathMapper):
             arvrunner.add_uploaded(src, (ab, st.fn))
             self._pathmap[src] = (ab, st.fn)
 
+        self.keepdir = None
+
+    def reversemap(self, target):
+        if target.startswith("keep:"):
+            return target
+        elif self.keepdir and target.startswith(self.keepdir):
+            return "keep:" + target[len(self.keepdir)+1:]
+        else:
+            return super(ArvPathMapper, self).reversemap(target)
 
 
 class ArvadosCommandTool(cwltool.draft2tool.CommandLineTool):