From 93ab6db3b62b69254a768c26477b0686d6afaa26 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 7 Dec 2020 10:25:22 -0600
Subject: [PATCH] Fix upload output bag ci unit test
---
.gitlab-ci.yml | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d4ee23b..6e7ee10 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -288,7 +288,7 @@ uploadInputBag:
script:
- ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
- >
- if [ `singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org ls /hatrac/resources/rnaseq/pipeline/input_bag/ | grep -q '/TEST$'` ]; then
+ if [ ! `singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org ls /hatrac/resources/rnaseq/pipeline/input_bag/ | grep -q '/TEST$'` ]; then
singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org mkdir /hatrac/resources/rnaseq/pipeline/input_bag/TEST
echo /hatrac/resources/rnaseq/pipeline/input_bag/TEST created
else
@@ -303,7 +303,7 @@ uploadInputBag:
cookie=$(cat credential.json | grep -A 1 '\"dev.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
cookie=${cookie:11:-1} &&
loc=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/input_bag/TEST/test.txt) &&
- rid=singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadInputBag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -o dev.gudmap.org -c ${cookie} &&
+ rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadInputBag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -o dev.gudmap.org -c ${cookie}) &&
echo ${rid} test input bag created
else
rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
@@ -382,7 +382,7 @@ uploadOutputBag:
cookie=$(cat credential.json | grep -A 1 '\"dev.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
cookie=${cookie:11:-1} &&
loc=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/output_bag/TEST/test.txt) &&
- rid=singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadOutputBag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -o dev.gudmap.org -c ${cookie} &&
+ rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadOutputBag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -o dev.gudmap.org -c ${cookie}) &&
echo ${rid} test output bag created
else
rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
--
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