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 39497098498792d1a4bb8595a77f6dcf9d1f6d47..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,
@@ -293,6 +296,12 @@ class Runner(object):
         self.tool = tool
         self.job_order = job_order
         self.running = False
+        if enable_reuse:
+            # If reuse is permitted by command line arguments but
+            # disabled by the workflow itself, disable it.
+            reuse_req, _ = get_feature(self.tool, "http://arvados.org/cwl#ReuseRequirement")
+            if reuse_req:
+                enable_reuse = reuse_req["enableReuse"]
         self.enable_reuse = enable_reuse
         self.uuid = None
         self.final_output = None