[ARVADOS] created: 1.1.4-760-g363094904

[Git user]

        at  363094904b570d223d59eb911150279308e98011 (commit)


commit 363094904b570d223d59eb911150279308e98011
Author: Lucas Di Pentima <ldipentima at veritasgenetics.com>
Date:   Wed Aug 8 17:13:30 2018 -0300

    13976: Fix keep reference error
    
    Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima at veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 3ad1aa6a7..a0617e1df 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -129,7 +129,8 @@ def upload_dependencies(arvrunner, name, document_loader,
 
     sc = []
     def only_real(obj):
-        if obj.get("location", "").startswith("file:"):
+        loc = obj.get("location", "")
+        if loc.startswith("file:") or loc.startswith("keep:"):
             sc.append(obj)
 
     visit_class(sc_result, ("File", "Directory"), only_real)

commit fdf14c1b9b4866c371fce9791c09b939194f3b6c
Author: Lucas Di Pentima <ldipentima at veritasgenetics.com>
Date:   Thu Aug 9 11:47:28 2018 -0300

    13976: Add CWL test exposing the bug
    
    Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima at veritasgenetics.com>

diff --git a/sdk/cwl/tests/13976-keepref-wf.cwl b/sdk/cwl/tests/13976-keepref-wf.cwl
new file mode 100644
index 000000000..7aa7b0aa4
--- /dev/null
+++ b/sdk/cwl/tests/13976-keepref-wf.cwl
@@ -0,0 +1,17 @@
+cwlVersion: v1.0
+class: CommandLineTool
+requirements:
+  - class: InlineJavascriptRequirement
+arguments:
+  - ls
+  - -l
+  - $(inputs.hello)
+inputs:
+  hello:
+    type: File
+    default:
+      class: File
+      location: keep:4d8a70b1e63b2aad6984e40e338e2373+69/hello.txt
+    secondaryFiles:
+      - .idx
+outputs: []
\ No newline at end of file
diff --git a/sdk/cwl/tests/arvados-tests.yml b/sdk/cwl/tests/arvados-tests.yml
index 21191a5b3..e51c7a253 100644
--- a/sdk/cwl/tests/arvados-tests.yml
+++ b/sdk/cwl/tests/arvados-tests.yml
@@ -120,6 +120,12 @@
 
 - job: null
   output:
+    out: null
+  tool: 13976-keepref-wf.cwl
+  doc: "Test issue 13976"
+
+- job: null
+  output:
     out: out
   tool: wf/runin-wf.cwl
   doc: "RunInSingleContainer cwl.input.json needs to be consistent with pathmapper manipulations"

-----------------------------------------------------------------------


hooks/post-receive
--