[ARVADOS] updated: 1.3.0-1060-gc7d692a3f
Git user
git at public.curoverse.com
Mon Jun 10 18:10:53 UTC 2019
Summary of changes:
sdk/cwl/arvados_cwl/runner.py | 2 +-
sdk/cwl/setup.py | 2 +-
sdk/cwl/tests/secondary/wf.cwl | 2 ++
sdk/cwl/tests/wf-defaults/wf6.cwl | 5 ++++-
sdk/cwl/tests/wf-defaults/wf7.cwl | 5 ++++-
sdk/cwl/tests/wf/runin-reqs-wf.cwl | 3 +++
sdk/cwl/tests/wf/runin-reqs-wf2.cwl | 3 +++
sdk/cwl/tests/wf/runin-reqs-wf4.cwl | 3 +++
sdk/cwl/tests/wf/runin-wf.cwl | 4 +++-
sdk/cwl/tests/wf/runin-with-ttl-wf.cwl | 4 +++-
10 files changed, 27 insertions(+), 6 deletions(-)
via c7d692a3f09d8116cc52591f8852c4e0d6e4ab3c (commit)
via d1a531b386641417d23f41115408d672f98c7e75 (commit)
via b670c0c80785770774e28a80d883dc258510bdb0 (commit)
via 9ee500be1e3dfd9a64214a14aba460108bcfa345 (commit)
from e7c542383a6364d422a14704a8ab11c96a976a41 (commit)
Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit c7d692a3f09d8116cc52591f8852c4e0d6e4ab3c
Merge: e7c542383 d1a531b38
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Mon Jun 10 14:10:36 2019 -0400
Merge branch '15028-fix-tests' refs #15028
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
commit d1a531b386641417d23f41115408d672f98c7e75
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Mon Jun 10 14:09:56 2019 -0400
15028: Fix test
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/sdk/cwl/tests/wf/runin-with-ttl-wf.cwl b/sdk/cwl/tests/wf/runin-with-ttl-wf.cwl
index e1d7fdfce..b81ad5a22 100644
--- a/sdk/cwl/tests/wf/runin-with-ttl-wf.cwl
+++ b/sdk/cwl/tests/wf/runin-with-ttl-wf.cwl
@@ -61,5 +61,5 @@ steps:
out:
type: string
outputBinding:
- outputEval: "out"
+ outputEval: $("out")
baseCommand: cat
commit b670c0c80785770774e28a80d883dc258510bdb0
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Mon Jun 10 11:37:12 2019 -0400
15028: Make sure tests use a version that supports CWL v1.1
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/sdk/cwl/tests/secondary/wf.cwl b/sdk/cwl/tests/secondary/wf.cwl
index 553956207..da9790e2d 100644
--- 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 6bcf69ed7..f607caa7f 100644
--- 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 715f1efcd..c2d4850f3 100644
--- 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 acaebb5d5..9d23c6a87 100644
--- 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 5795759d9..2701fd1c8 100644
--- 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 fc06fb30a..9a26d0113 100644
--- 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-with-ttl-wf.cwl b/sdk/cwl/tests/wf/runin-with-ttl-wf.cwl
index 713e0c06c..e1d7fdfce 100644
--- 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:
commit 9ee500be1e3dfd9a64214a14aba460108bcfa345
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Fri Jun 7 15:27:05 2019 -0400
15028: Bump cwltool version for bugfix.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 183e21cf9..912faf0e8 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 b1c7b90b0..ceea719ef 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 a192b8648..68a26a0d3 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
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