X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/3854e6bfcd5344bce5ee0388248cb115e3c5e902..2a3daf14afb93de4d65108019a7a1d35aa1052ad:/sdk/cwl/arvados_cwl/runner.py

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 3949709849..28de7f368a 100644
--- 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