[ARVADOS] updated: ca1219da20b4460ec6b9e2c9474981412964d9b3
Git user
git at public.curoverse.com
Mon Oct 2 14:26:28 EDT 2017
Summary of changes:
sdk/cwl/tests/12213-keepref-expr.cwl | 4 ++--
sdk/cwl/tests/12213-keepref-tool.cwl | 4 +++-
sdk/cwl/tests/12213-keepref-wf.cwl | 7 +++++--
sdk/cwl/tests/arvados-tests.sh | 2 +-
sdk/cwl/tests/arvados-tests.yml | 17 ++++++++++++++++-
sdk/cwl/tests/runner.sh | 6 ------
6 files changed, 27 insertions(+), 13 deletions(-)
delete mode 100755 sdk/cwl/tests/runner.sh
via ca1219da20b4460ec6b9e2c9474981412964d9b3 (commit)
from a06dc44e3acd3844096ebb5829780877145c4424 (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 ca1219da20b4460ec6b9e2c9474981412964d9b3
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Oct 2 14:25:42 2017 -0400
12213: Check for correct test output.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/sdk/cwl/tests/12213-keepref-expr.cwl b/sdk/cwl/tests/12213-keepref-expr.cwl
index c28f7e8..ddc7ff9 100644
--- a/sdk/cwl/tests/12213-keepref-expr.cwl
+++ b/sdk/cwl/tests/12213-keepref-expr.cwl
@@ -22,10 +22,10 @@ expression: |
}
}
var dirs = [];
- for (var sampleid in samples) {
+ Object.keys(samples).sort().forEach(function(sampleid, _) {
dirs.push({"class": "Directory",
"basename": sampleid,
"listing": samples[sampleid]});
- }
+ });
return {"out": dirs};
}
\ No newline at end of file
diff --git a/sdk/cwl/tests/12213-keepref-tool.cwl b/sdk/cwl/tests/12213-keepref-tool.cwl
index 4e55875..8c28cc2 100644
--- a/sdk/cwl/tests/12213-keepref-tool.cwl
+++ b/sdk/cwl/tests/12213-keepref-tool.cwl
@@ -4,8 +4,10 @@ requirements:
InlineJavascriptRequirement: {}
inputs:
fastqsdir: Directory
-outputs: []
+outputs:
+ out: stdout
baseCommand: [zcat]
+stdout: $(inputs.fastqsdir.listing[0].nameroot).txt
arguments:
- $(inputs.fastqsdir.listing[0].path)
- $(inputs.fastqsdir.listing[1].path)
diff --git a/sdk/cwl/tests/12213-keepref-wf.cwl b/sdk/cwl/tests/12213-keepref-wf.cwl
index 0c8427a..3f1e890 100644
--- a/sdk/cwl/tests/12213-keepref-wf.cwl
+++ b/sdk/cwl/tests/12213-keepref-wf.cwl
@@ -4,7 +4,10 @@ requirements:
ScatterFeatureRequirement: {}
inputs:
dir: Directory
-outputs: []
+outputs:
+ out:
+ type: File[]
+ outputSource: tool/out
steps:
ex:
in:
@@ -14,6 +17,6 @@ steps:
tool:
in:
fastqsdir: ex/out
- out: []
+ out: [out]
scatter: fastqsdir
run: 12213-keepref-tool.cwl
\ No newline at end of file
diff --git a/sdk/cwl/tests/arvados-tests.sh b/sdk/cwl/tests/arvados-tests.sh
index f069251..f7cebd4 100755
--- a/sdk/cwl/tests/arvados-tests.sh
+++ b/sdk/cwl/tests/arvados-tests.sh
@@ -6,4 +6,4 @@
if ! arv-get d7514270f356df848477718d58308cc4+94 > /dev/null ; then
arv-put --portable-data-hash testdir
fi
-exec cwltest --test arvados-tests.yml --tool $PWD/runner.sh $@
+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 35efab4..2f1429e 100644
--- a/sdk/cwl/tests/arvados-tests.yml
+++ b/sdk/cwl/tests/arvados-tests.yml
@@ -93,6 +93,21 @@
doc: "Test arv:ReuseRequirement"
- job: 12213-keepref-job.yml
- output: {}
+ output: {
+ "out": [
+ {
+ "checksum": "sha1$1c78028c0d69163391eef89316b44a57bde3fead",
+ "location": "sample1_S01_R1_001.fastq.txt",
+ "class": "File",
+ "size": 32
+ },
+ {
+ "checksum": "sha1$83483b9c65d99967aecc794c14f9f4743314d186",
+ "location": "sample2_S01_R3_001.fastq.txt",
+ "class": "File",
+ "size": 32
+ }
+ ]
+ }
tool: 12213-keepref-wf.cwl
doc: "Test manipulating keep references with expression tools"
diff --git a/sdk/cwl/tests/runner.sh b/sdk/cwl/tests/runner.sh
deleted file mode 100755
index 20bbb26..0000000
--- a/sdk/cwl/tests/runner.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/sh
-# Copyright (C) The Arvados Authors. All rights reserved.
-#
-# SPDX-License-Identifier: Apache-2.0
-
-exec arvados-cwl-runner --disable-reuse --compute-checksum "$@"
-----------------------------------------------------------------------
hooks/post-receive
--
More information about the arvados-commits
mailing list