From: Peter Amstutz <pamstutz@veritasgenetics.com>
Date: Fri, 7 Jun 2019 19:27:05 +0000 (-0400)
Subject: 15028: Bump cwltool version for bugfix.
X-Git-Tag: 2.0.0~307^2~2
X-Git-Url: https://git.arvados.org/arvados.git/commitdiff_plain/9ee500be1e3dfd9a64214a14aba460108bcfa345

15028: Bump cwltool version for bugfix.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
---

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 183e21cf95..912faf0e87 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -174,7 +174,7 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
             if pattern is None:
                 continue
             sfpath = substitute(primary["location"], pattern)
-            required = builder.do_eval(sf["required"], context=primary)
+            required = builder.do_eval(sf.get("required"), context=primary)
 
             if fsaccess.exists(sfpath):
                 primary["secondaryFiles"].append({"location": sfpath, "class": "File"})
diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index b1c7b90b0d..ceea719efe 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -33,7 +33,7 @@ setup(name='arvados-cwl-runner',
       # Note that arvados/build/run-build-packages.sh looks at this
       # file to determine what version of cwltool and schema-salad to build.
       install_requires=[
-          'cwltool==1.0.20190603140227',
+          'cwltool==1.0.20190607183319',
           'schema-salad==4.2.20190417121603',
           'typing >= 3.6.4',
           'ruamel.yaml >=0.15.54, <=0.15.77',
diff --git a/sdk/cwl/tests/wf/runin-wf.cwl b/sdk/cwl/tests/wf/runin-wf.cwl
index a192b86488..68a26a0d36 100644
--- a/sdk/cwl/tests/wf/runin-wf.cwl
+++ b/sdk/cwl/tests/wf/runin-wf.cwl
@@ -35,6 +35,8 @@ steps:
     out: [out]
     hints:
       - class: arv:RunInSingleContainer
+      - class: DockerRequirement
+        dockerPull: arvados/jobs:1.4.0.20190604172024
     run:
       class: Workflow
       id: mysub
@@ -60,5 +62,5 @@ steps:
               out:
                 type: string
                 outputBinding:
-                  outputEval: "out"
+                  outputEval: $("out")
             baseCommand: cat