[ARVADOS] updated: ca1219da20b4460ec6b9e2c9474981412964d9b3

[Git user]

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$83483b9c65d99967aecc794c14f9f4743314d186",
+            "location": "sample2_S01_R3_001.fastq.txt",
+            "class": "File",
+            "size": 32
+        }
+    ]
+  }
   tool: 12213-keepref-wf.cwl
   doc: "Test manipulating keep references with expression tools"
diff --git a/sdk/cwl/tests/runner.sh b/sdk/cwl/tests/runner.sh
deleted file mode 100755
index 20bbb26..0000000
--- a/sdk/cwl/tests/runner.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/sh
-# Copyright (C) The Arvados Authors. All rights reserved.
-#
-# SPDX-License-Identifier: Apache-2.0
-
-exec arvados-cwl-runner --disable-reuse --compute-checksum "$@"

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