From c8efb567a34fa646837d2231120a8465e93dc02b Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 30 Nov 2020 16:37:32 -0600
Subject: [PATCH] Fix CI unit uploadInputBag
---
.gitlab-ci.yml | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b2eae12..eb96c17 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -287,16 +287,16 @@ uploadInputBag:
- merge_requests
script:
- ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
- - hatrac=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org ls /hatrac/resources/rnaseq/pipeline/input_bag/ | grep -o /TEST$)
- >
+ hatrac=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org ls /hatrac/resources/rnaseq/pipeline/input_bag/ | grep -o /TEST$) &&
if [ -z "${hatrac}" ]; then
singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org mkdir /hatrac/resources/rnaseq/pipeline/input_bag/TEST
fi
- echo THIS IS A TEST FILE > test.txt
- - md5=$(md5sum ./test.txt | awk '{ print $1 }')
- - size=$(wc -c < ./test.txt)
- - exist=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' curl -s https://dev.gudmap.org/ermrest/catalog/2/entity/RNASeq:Input_Bag/File_MD5=${md5})
- >
+ md5=$(md5sum ./test.txt | awk '{ print $1 }')
+ size=$(wc -c < ./test.txt)
+ exist=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' curl -s https://dev.gudmap.org/ermrest/catalog/2/entity/RNASeq:Input_Bag/File_MD5=${md5})
if [ "${exist}" == "[]" ]; then
cookie=$(cat credential.json | grep -A 1 '\"dev.gudmap.org\": {' | grep -o '\"cookie\": \".*\"')
cookie=${cookie:11:-1}
--
GitLab