12913: Apply secondaryFiles to inputs to RunInSingleContainer

[arvados.git] / sdk / cwl / arvados_cwl / runner.py

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index c55e976924f65bd362153a0921152e5a170ca47b..28de7f368a23ccbc52a0cae37fa55d358744d0e1 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -191,12 +191,8 @@ def tag_git_version(packed):
             packed["http://schema.org/version"] = githash
 
 
-def upload_job_order(arvrunner, name, tool, job_order):
-    """Upload local files referenced in the input object and return updated input
-    object with 'location' updated to the proper keep references.
-    """
-
-    for t in tool.tool["inputs"]:
+def discover_secondary_files(inputs, job_order):
+    for t in inputs:
         def setSecondary(fileobj):
             if isinstance(fileobj, dict) and fileobj.get("class") == "File":
                 if "secondaryFiles" not in fileobj:
@@ -209,6 +205,13 @@ def upload_job_order(arvrunner, name, tool, job_order):
         if shortname(t["id"]) in job_order and t.get("secondaryFiles"):
             setSecondary(job_order[shortname(t["id"])])
 
+def upload_job_order(arvrunner, name, tool, job_order):
+    """Upload local files referenced in the input object and return updated input
+    object with 'location' updated to the proper keep references.
+    """
+
+    discover_secondary_files(tool.tool["inputs"], job_order)
+
     jobmapper = upload_dependencies(arvrunner,
                                     name,
                                     tool.doc_loader,