[ARVADOS] updated: 1.1.3-208-g6018e31

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/__init__.py     | 2 +-
 sdk/cwl/arvados_cwl/arvcontainer.py | 7 +++++++
 2 files changed, 8 insertions(+), 1 deletion(-)

       via  6018e31ef8c2d344be0d596a1e8ca11d95bf0870 (commit)
      from  16feb1a87c3e2e1955ad45caad0bd4b531f1cb26 (commit)

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commit 6018e31ef8c2d344be0d596a1e8ca11d95bf0870
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Wed Mar 14 10:48:58 2018 -0400

    13135: Code cleanup & comments.
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 2792b30..e4f5cea 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 704bda6..39b9c24 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,

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