14198: Fix secondaryFile tests

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/arvtool.py b/sdk/cwl/arvados_cwl/arvtool.py
index ee9dd25a13f2261754c1d31e8b92fce545b641cd..8167edc57449eef8d1571900747d2a30cef8df3c 100644 (file)
--- 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 218006633851342d0e49e9674826d099cbad2245..4cc01a91ce80e08aca68af320a03c8b199d2b3fe 100644 (file)
--- 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)