14198: Set arvrunner on ArvadosWorkflowStep

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 130b42b5cc4ae1ded368a4cf4cfdc748532887d1..1a0c81b2830ee6082322d77d8395ee8ee79a0432 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvtool.py
+++ b/sdk/cwl/arvados_cwl/arvtool.py
@@ -6,7 +6,6 @@ from cwltool.command_line_tool import CommandLineTool
 from .arvjob import ArvadosJob
 from .arvcontainer import ArvadosContainer
 from .pathmapper import ArvPathMapper
-from .context import ClusterTarget
 from functools import partial
 from schema_salad.sourceline import SourceLine
 from cwltool.errors import WorkflowException

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index f06d569bf3219429ae61ac04744051504aa8975a..5f4f8867a46d3373b2307f4266356427112b1114 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -123,12 +123,14 @@ class ArvadosWorkflowStep(WorkflowStep):
                  toolpath_object,      # type: Dict[Text, Any]
                  pos,                  # type: int
                  loadingContext,       # type: LoadingContext
+                 arvrunner,
                  *argc,
                  **argv
                 ):  # type: (...) -> None
 
         super(ArvadosWorkflowStep, self).__init__(toolpath_object, pos, loadingContext, *argc, **argv)
         self.tool["class"] = "WorkflowStep"
+        self.arvrunner = arvrunner
 
     def job(self, joborder, output_callback, runtimeContext):
         builder = self._init_job({shortname(k): v for k,v in joborder.items()}, runtimeContext)
@@ -308,4 +310,4 @@ class ArvadosWorkflow(Workflow):
                            **argv
     ):
         # (...) -> WorkflowStep
-        return ArvadosWorkflowStep(toolpath_object, pos, loadingContext, *argc, **argv)
+        return ArvadosWorkflowStep(toolpath_object, pos, loadingContext, self.arvrunner, *argc, **argv)

diff --git a/sdk/cwl/arvados_cwl/context.py b/sdk/cwl/arvados_cwl/context.py
index 8af3f20c863fccc0cb252d70d19dcac8a44733dd..7831e1cfd0822abbcac5a77c460a33e8ff492714 100644 (file)
--- a/sdk/cwl/arvados_cwl/context.py
+++ b/sdk/cwl/arvados_cwl/context.py
@@ -9,8 +9,6 @@ class ArvLoadingContext(LoadingContext):
     def __init__(self, kwargs=None):
         super(ArvLoadingContext, self).__init__(kwargs)
 
-ClusterTarget = namedtuple("ClusterTarget", ("instance", "cluster_id", "owner_uuid"))
-
 class ArvRuntimeContext(RuntimeContext):
     def __init__(self, kwargs=None):
         self.work_api = None