16353: Initialize 'builder' with document version

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

diff --git a/sdk/cwl/arvados_cwl/arvtool.py b/sdk/cwl/arvados_cwl/arvtool.py
index 704edaccb903eb83f1e66c983eb007fe1c4f8711..a9361a85f9fe66a5260a64b6719fa74c28cdeee2 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvtool.py
+++ b/sdk/cwl/arvados_cwl/arvtool.py
@@ -57,7 +57,7 @@ class ArvadosCommandTool(CommandLineTool):
                                  "/keep/%s/%s")
 
     def job(self, joborder, output_callback, runtimeContext):
-        builder = make_builder(joborder, self.hints, self.requirements, runtimeContext)
+        builder = make_builder(joborder, self.hints, self.requirements, runtimeContext, self.metadata)
         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 ddd3c00764c7b0fb42fe97adf50622bd1b23e9cb..97c5fafe792fc06ce099e6a9bc6934671ace580d 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -141,7 +141,8 @@ class ArvadosWorkflowStep(WorkflowStep):
         runtimeContext = runtimeContext.copy()
         runtimeContext.toplevel = True  # Preserve behavior for #13365
 
-        builder = make_builder({shortname(k): v for k,v in viewitems(joborder)}, self.hints, self.requirements, runtimeContext)
+        builder = make_builder({shortname(k): v for k,v in viewitems(joborder)}, self.hints, self.requirements,
+                               runtimeContext, self.metadata)
         runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext)
         return super(ArvadosWorkflowStep, self).job(joborder, output_callback, runtimeContext)
 
@@ -161,7 +162,7 @@ class ArvadosWorkflow(Workflow):
 
     def job(self, joborder, output_callback, runtimeContext):
 
-        builder = make_builder(joborder, self.hints, self.requirements, runtimeContext)
+        builder = make_builder(joborder, self.hints, self.requirements, runtimeContext, self.metadata)
         runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext)
 
         req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer")

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 71e499ebcab0cca29ccbee7a350cfbbb5aaa6e19..8540b6d245e5a823c137f2cf351da711eae52807 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -83,7 +83,7 @@ def find_defaults(d, op):
             for i in viewvalues(d):
                 find_defaults(i, op)
 
-def make_builder(joborder, hints, requirements, runtimeContext):
+def make_builder(joborder, hints, requirements, runtimeContext, metadata):
     return Builder(
                  job=joborder,
                  files=[],               # type: List[Dict[Text, Text]]
@@ -106,6 +106,7 @@ def make_builder(joborder, hints, requirements, runtimeContext):
                  outdir="",              # type: Text
                  tmpdir="",              # type: Text
                  stagedir="",            # type: Text
+                 cwlVersion=metadata.get("http://commonwl.org/cwltool#original_cwlVersion")
                 )
 
 def search_schemadef(name, reqs):
@@ -354,7 +355,8 @@ def upload_dependencies(arvrunner, name, document_loader,
         builder = make_builder(builder_job_order,
                                obj.get("hints", []),
                                obj.get("requirements", []),
-                               ArvRuntimeContext())
+                               ArvRuntimeContext(),
+                               {})
         discover_secondary_files(arvrunner.fs_access,
                                  builder,
                                  obj["inputs"],
@@ -516,7 +518,8 @@ def upload_job_order(arvrunner, name, tool, job_order):
     builder = make_builder(builder_job_order,
                            tool.hints,
                            tool.requirements,
-                           ArvRuntimeContext())
+                           ArvRuntimeContext(),
+                           tool.metadata)
     # Now update job_order with secondaryFiles
     discover_secondary_files(arvrunner.fs_access,
                              builder,