[ARVADOS] updated: 1.2.0-424-ge2f3e9115

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/arvtool.py     | 10 +---------
 sdk/cwl/arvados_cwl/arvworkflow.py |  3 +++
 2 files changed, 4 insertions(+), 9 deletions(-)

       via  e2f3e91154c05ce5f4bf0724c3a05a5ccf24edda (commit)
      from  423936db5b43ba7b60a9088d5b0be80e1dee0599 (commit)

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commit e2f3e91154c05ce5f4bf0724c3a05a5ccf24edda
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Mon Nov 19 15:05:01 2018 -0500

    14198: Fix secondaryFile tests
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/arvtool.py b/sdk/cwl/arvados_cwl/arvtool.py
index ee9dd25a1..8167edc57 100644
--- a/sdk/cwl/arvados_cwl/arvtool.py
+++ b/sdk/cwl/arvados_cwl/arvtool.py
@@ -57,15 +57,7 @@ class ArvadosCommandTool(CommandLineTool):
                                  "$(task.keep)/%s/%s")
 
     def job(self, joborder, output_callback, runtimeContext):
-
-        # Workaround for #13365
-        builderargs = runtimeContext.copy()
-        builderargs.toplevel = True
-        builderargs.tmp_outdir_prefix = ""
-        builder = self._init_job(joborder, builderargs)
-        joborder = builder.job
-
-        runtimeContext = runtimeContext.copy()
+        builder = self._init_job(joborder, runtimeContext)
         runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext)
 
         if runtimeContext.work_api == "containers":
diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index 218006633..4cc01a91c 100644
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -133,6 +133,9 @@ class ArvadosWorkflowStep(WorkflowStep):
         self.arvrunner = arvrunner
 
     def job(self, joborder, output_callback, runtimeContext):
+        runtimeContext = runtimeContext.copy()
+        runtimeContext.toplevel = True  # Preserve behavior for #13365
+
         builder = self._init_job({shortname(k): v for k,v in joborder.items()}, runtimeContext)
         runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext)
         return super(ArvadosWorkflowStep, self).job(joborder, output_callback, runtimeContext)

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