From 423364e3772de59ca4638388605fd556a2a0da3e Mon Sep 17 00:00:00 2001
From: Peter Amstutz <pamstutz@veritasgenetics.com>
Date: Wed, 15 Nov 2017 13:34:32 -0500
Subject: [PATCH] 12601: Add test

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
---
 sdk/cwl/tests/arvados-tests.sh  |  2 +-
 sdk/cwl/tests/arvados-tests.yml |  6 ++++
 sdk/cwl/tests/wf/runin-wf.cwl   | 64 +++++++++++++++++++++++++++++++++
 3 files changed, 71 insertions(+), 1 deletion(-)
 create mode 100644 sdk/cwl/tests/wf/runin-wf.cwl

diff --git a/sdk/cwl/tests/arvados-tests.sh b/sdk/cwl/tests/arvados-tests.sh
index f7cebd4249..26b31615ea 100755
--- a/sdk/cwl/tests/arvados-tests.sh
+++ b/sdk/cwl/tests/arvados-tests.sh
@@ -4,6 +4,6 @@
 # SPDX-License-Identifier: Apache-2.0
 
 if ! arv-get d7514270f356df848477718d58308cc4+94 > /dev/null ; then
-    arv-put --portable-data-hash testdir
+    arv-put --portable-data-hash testdir/*
 fi
 exec cwltest --test arvados-tests.yml --tool arvados-cwl-runner $@ -- --disable-reuse --compute-checksum
diff --git a/sdk/cwl/tests/arvados-tests.yml b/sdk/cwl/tests/arvados-tests.yml
index a0de23694c..f6271b85d2 100644
--- a/sdk/cwl/tests/arvados-tests.yml
+++ b/sdk/cwl/tests/arvados-tests.yml
@@ -117,3 +117,9 @@
     out: null
   tool: 12418-glob-empty-collection.cwl
   doc: "Test glob output on empty collection"
+
+- job: null
+  output:
+    out: out
+  tool: wf/runin-wf.cwl
+  doc: "RunInSingleContainer cwl.input.json needs to be consistent with pathmapper manipulations"
diff --git a/sdk/cwl/tests/wf/runin-wf.cwl b/sdk/cwl/tests/wf/runin-wf.cwl
new file mode 100644
index 0000000000..a192b86488
--- /dev/null
+++ b/sdk/cwl/tests/wf/runin-wf.cwl
@@ -0,0 +1,64 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+class: Workflow
+cwlVersion: v1.0
+$namespaces:
+  arv: "http://arvados.org/cwl#"
+inputs:
+  sleeptime:
+    type: int
+    default: 5
+  fileblub:
+    type: File
+    default:
+      class: File
+      location: keep:d7514270f356df848477718d58308cc4+94/a
+      secondaryFiles:
+        - class: File
+          location: keep:d7514270f356df848477718d58308cc4+94/b
+outputs:
+  out:
+    type: string
+    outputSource: substep/out
+requirements:
+  SubworkflowFeatureRequirement: {}
+  ScatterFeatureRequirement: {}
+  InlineJavascriptRequirement: {}
+  StepInputExpressionRequirement: {}
+steps:
+  substep:
+    in:
+      sleeptime: sleeptime
+      fileblub: fileblub
+    out: [out]
+    hints:
+      - class: arv:RunInSingleContainer
+    run:
+      class: Workflow
+      id: mysub
+      inputs:
+        fileblub: File
+      outputs:
+        out:
+          type: string
+          outputSource: sleep1/out
+      steps:
+        sleep1:
+          in:
+            fileblub: fileblub
+          out: [out]
+          run:
+            class: CommandLineTool
+            id: subtool
+            inputs:
+              fileblub:
+                type: File
+                inputBinding: {position: 1}
+            outputs:
+              out:
+                type: string
+                outputBinding:
+                  outputEval: "out"
+            baseCommand: cat
-- 
2.30.2