Merge branch '9307-cwl-use-tmp-output' closes #9307 closes #9308

[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 413435db2392e38aa22ba0d5222fef333080dbde..fa32456c3f2c6b4a9e0a4f455a8662a8ea2fc42d 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -90,6 +90,14 @@ class ArvadosContainer(object):
             runtime_constraints["vcpus"] = resources.get("cores", 1)
             runtime_constraints["ram"] = resources.get("ram") * 2**20
 
+        api_req, _ = get_feature(self, "http://arvados.org/cwl#APIRequirement")
+        if api_req:
+            runtime_constraints["API"] = True
+
+        runtime_req, _ = get_feature(self, "http://arvados.org/cwl#RuntimeConstraints")
+        if runtime_req:
+            logger.warn("RuntimeConstraints not yet supported by container API")
+
         container_request["mounts"] = mounts
         container_request["runtime_constraints"] = runtime_constraints
 
@@ -153,7 +161,9 @@ class RunnerContainer(Runner):
 
         workflowmapper = super(RunnerContainer, self).arvados_job_spec(dry_run=dry_run, pull_image=pull_image, **kwargs)
 
-        with arvados.collection.Collection(api_client=self.arvrunner.api) as jobobj:
+        with arvados.collection.Collection(api_client=self.arvrunner.api,
+                                           keep_client=self.arvrunner.keep_client,
+                                           num_retries=self.arvrunner.num_retries) as jobobj:
             with jobobj.open("cwl.input.json", "w") as f:
                 json.dump(self.job_order, f, sort_keys=True, indent=4)
             jobobj.save_new(owner_uuid=self.arvrunner.project_uuid)
@@ -169,8 +179,13 @@ class RunnerContainer(Runner):
                                                pull_image,
                                                self.arvrunner.project_uuid)
 
+        command = ["arvados-cwl-runner", "--local", "--api=containers"]
+        if self.output_name:
+            command.append("--output-name=" + self.output_name)
+        command.extend([workflowpath, jobpath])
+
         return {
-            "command": ["arvados-cwl-runner", "--local", "--api=containers", workflowpath, jobpath],
+            "command": command,
             "owner_uuid": self.arvrunner.project_uuid,
             "name": self.name,
             "output_path": "/var/spool/cwl",