[ARVADOS] updated: 1.1.4-761-g32d403dd4

Git user git at public.curoverse.com
Fri Aug 10 10:15:55 EDT 2018


Summary of changes:
 sdk/cwl/arvados_cwl/runner.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

       via  32d403dd4d791e88ee93ddda7865a1566e3da116 (commit)
      from  363094904b570d223d59eb911150279308e98011 (commit)

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commit 32d403dd4d791e88ee93ddda7865a1566e3da116
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Fri Aug 10 10:14:31 2018 -0400

    13976: Filter out keep references with secondaryFiles from list of files to upload
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index a0617e1df..79be88191 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -129,8 +129,7 @@ def upload_dependencies(arvrunner, name, document_loader,
 
     sc = []
     def only_real(obj):
-        loc = obj.get("location", "")
-        if loc.startswith("file:") or loc.startswith("keep:"):
+        if obj.get("location", "").startswith("file:"):
             sc.append(obj)
 
     visit_class(sc_result, ("File", "Directory"), only_real)
@@ -169,8 +168,13 @@ def upload_dependencies(arvrunner, name, document_loader,
 
     visit_class(workflowobj, ("CommandLineTool", "Workflow"), discover_default_secondary_files)
 
-    for d in discovered:
-        sc.extend(discovered[d])
+    for d in list(discovered.keys()):
+        # Only interested in discovered secondaryFiles which are local
+        # files that need to be uploaded.
+        if d.startswith("file:"):
+            sc.extend(discovered[d])
+        else:
+            del discovered[d]
 
     mapper = ArvPathMapper(arvrunner, sc, "",
                            "keep:%s",

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