From 6018e31ef8c2d344be0d596a1e8ca11d95bf0870 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Wed, 14 Mar 2018 10:48:58 -0400 Subject: [PATCH] 13135: Code cleanup & comments. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- sdk/cwl/arvados_cwl/__init__.py | 2 +- sdk/cwl/arvados_cwl/arvcontainer.py | 7 +++++++ 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py index 2792b30fbd..e4f5ceab74 100644 --- a/sdk/cwl/arvados_cwl/__init__.py +++ b/sdk/cwl/arvados_cwl/__init__.py @@ -455,7 +455,7 @@ class ArvCwlRunner(object): intermediate_output_ttl=kwargs.get("intermediate_output_ttl"), merged_map=merged_map, priority=kwargs.get("priority"), - secret_store=kwargs.get("secret_store")) + secret_store=self.secret_store) elif self.work_api == "jobs": runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name, diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py index 704bda6ebc..39b9c2416a 100644 --- a/sdk/cwl/arvados_cwl/arvcontainer.py +++ b/sdk/cwl/arvados_cwl/arvcontainer.py @@ -42,6 +42,13 @@ class ArvadosContainer(object): pass def run(self, dry_run=False, pull_image=True, **kwargs): + # ArvadosCommandTool subclasses from cwltool.CommandLineTool, + # which calls makeJobRunner() to get a new ArvadosContainer + # object. The fields that define execution such as + # command_line, environment, etc are set on the + # ArvadosContainer object by CommandLineTool.job() before + # run() is called. + container_request = { "command": self.command_line, "owner_uuid": self.arvrunner.project_uuid, -- 2.30.2