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 183e21cf95b01c046ea3acbbad2bc94f39fa41f5..912faf0e875b45655de56355374cca025bcc7377 100644 (file)
--- 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)
             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"})
 
             if fsaccess.exists(sfpath):
                 primary["secondaryFiles"].append({"location": sfpath, "class": "File"})

diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index b1c7b90b0d9c66464c81f30986c63e86c4c101d7..ceea719efe3f3f8a539dd9c9079d67bb93b588e4 100644 (file)
--- 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=[
       # 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',
           '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 a192b86488703187ec2ffb8f4e186693b0ec18df..68a26a0d361a36fe609b981af3b180901a632331 100644 (file)
--- 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
     out: [out]
     hints:
       - class: arv:RunInSingleContainer

+      - class: DockerRequirement
+        dockerPull: arvados/jobs:1.4.0.20190604172024

     run:
       class: Workflow
       id: mysub
     run:
       class: Workflow
       id: mysub


@@ -60,5 +62,5 @@ steps:
               out:
                 type: string
                 outputBinding:
               out:
                 type: string
                 outputBinding:

-                  outputEval: "out"
+                  outputEval: $("out")

             baseCommand: cat
             baseCommand: cat