Merge branch '15028-fix-tests' refs #15028

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)
-            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 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=[
-          '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/secondary/wf.cwl b/sdk/cwl/tests/secondary/wf.cwl
index 5539562070ff2c226b8188f66df8a452af7f59a8..da9790e2d0f3913bed05fd87bdc17a79d6ab92e5 100644 (file)
--- a/sdk/cwl/tests/secondary/wf.cwl
+++ b/sdk/cwl/tests/secondary/wf.cwl
@@ -9,6 +9,8 @@ $namespaces:
   cwltool: "http://commonwl.org/cwltool#"
 requirements:
   SubworkflowFeatureRequirement: {}
+  DockerRequirement:
+    dockerPull: arvados/jobs:1.4.0.20190604172024
 inputs:
   i:
     type: File

diff --git a/sdk/cwl/tests/wf-defaults/wf6.cwl b/sdk/cwl/tests/wf-defaults/wf6.cwl
index 6bcf69ed7fcd50561377878d7e1da9efca7a6240..f607caa7fa7f214425e5b6559b3488bd6e83bc1a 100644 (file)
--- a/sdk/cwl/tests/wf-defaults/wf6.cwl
+++ b/sdk/cwl/tests/wf-defaults/wf6.cwl
@@ -10,10 +10,13 @@ $namespaces:
   arv: "http://arvados.org/cwl#"
 requirements:
   SubworkflowFeatureRequirement: {}
+hints:
+  DockerRequirement:
+    dockerPull: arvados/jobs:1.4.0.20190604172024
 steps:
   step1:
     requirements:
       arv:RunInSingleContainer: {}
     in: []
     out: []
-    run: default-dir6.cwl
\ No newline at end of file
+    run: default-dir6.cwl

diff --git a/sdk/cwl/tests/wf-defaults/wf7.cwl b/sdk/cwl/tests/wf-defaults/wf7.cwl
index 715f1efcdfb542065faf11bc208463918a9a3c88..c2d4850f3526d1b3f466235f282bd8a9e9fb1e16 100644 (file)
--- a/sdk/cwl/tests/wf-defaults/wf7.cwl
+++ b/sdk/cwl/tests/wf-defaults/wf7.cwl
@@ -10,10 +10,13 @@ $namespaces:
   arv: "http://arvados.org/cwl#"
 requirements:
   SubworkflowFeatureRequirement: {}
+hints:
+  DockerRequirement:
+    dockerPull: arvados/jobs:1.4.0.20190604172024
 steps:
   step1:
     requirements:
       arv:RunInSingleContainer: {}
     in: []
     out: []
-    run: default-dir7.cwl
\ No newline at end of file
+    run: default-dir7.cwl

diff --git a/sdk/cwl/tests/wf/runin-reqs-wf.cwl b/sdk/cwl/tests/wf/runin-reqs-wf.cwl
index acaebb5d58b491a390b48e3064701b8a52331c31..9d23c6a87e69d1502d073b59424a92574519cc7a 100644 (file)
--- a/sdk/cwl/tests/wf/runin-reqs-wf.cwl
+++ b/sdk/cwl/tests/wf/runin-reqs-wf.cwl
@@ -22,6 +22,9 @@ requirements:
   ScatterFeatureRequirement: {}
   InlineJavascriptRequirement: {}
   StepInputExpressionRequirement: {}
+hints:
+  DockerRequirement:
+    dockerPull: arvados/jobs:1.4.0.20190604172024
 steps:
   substep:
     in:

diff --git a/sdk/cwl/tests/wf/runin-reqs-wf2.cwl b/sdk/cwl/tests/wf/runin-reqs-wf2.cwl
index 5795759d9fcf30a33bc86f6f222d5363d34df71f..2701fd1c85991cc018b69a568fb8161dc520321f 100644 (file)
--- a/sdk/cwl/tests/wf/runin-reqs-wf2.cwl
+++ b/sdk/cwl/tests/wf/runin-reqs-wf2.cwl
@@ -22,6 +22,9 @@ requirements:
   ScatterFeatureRequirement: {}
   InlineJavascriptRequirement: {}
   StepInputExpressionRequirement: {}
+hints:
+  DockerRequirement:
+    dockerPull: arvados/jobs:1.4.0.20190604172024
 steps:
   substep:
     in:

diff --git a/sdk/cwl/tests/wf/runin-reqs-wf4.cwl b/sdk/cwl/tests/wf/runin-reqs-wf4.cwl
index fc06fb30a6157a5a393764029a7d9d9d22c3c8e3..9a26d01132cf07d6ae1cb11aff97a627807ddca5 100644 (file)
--- a/sdk/cwl/tests/wf/runin-reqs-wf4.cwl
+++ b/sdk/cwl/tests/wf/runin-reqs-wf4.cwl
@@ -22,6 +22,9 @@ requirements:
   ScatterFeatureRequirement: {}
   InlineJavascriptRequirement: {}
   StepInputExpressionRequirement: {}
+hints:
+  DockerRequirement:
+    dockerPull: arvados/jobs:1.4.0.20190604172024
 steps:
   substep:
     in:

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
+      - 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

diff --git a/sdk/cwl/tests/wf/runin-with-ttl-wf.cwl b/sdk/cwl/tests/wf/runin-with-ttl-wf.cwl
index 713e0c06cf10bbcad0308144f7a5dc4b56f7601e..b81ad5a22e3ab5cb8e2981fce56c4dec21341373 100644 (file)
--- a/sdk/cwl/tests/wf/runin-with-ttl-wf.cwl
+++ b/sdk/cwl/tests/wf/runin-with-ttl-wf.cwl
@@ -27,6 +27,8 @@ requirements:
 hints:
   arv:IntermediateOutput:
     outputTTL: 60
+  DockerRequirement:
+    dockerPull: arvados/jobs:1.4.0.20190604172024
 steps:
   substep:
     in:
@@ -59,5 +61,5 @@ steps:
               out:
                 type: string
                 outputBinding:
-                  outputEval: "out"
+                  outputEval: $("out")
             baseCommand: cat