From 33993f7563832323e40824a036cdfed170c97fc7 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 30 Nov 2020 16:23:50 -0600
Subject: [PATCH] Change uploadInputBag unit test to use new singularity
container
---
.gitlab-ci.yml | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 1907204..aba54e7 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -287,21 +287,21 @@ uploadInputBag:
- merge_requests
script:
- ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
- - hatrac=$(singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-hatrac-cli --host dev.gudmap.org ls /hatrac/resources/rnaseq/pipeline/input_bag/ | grep -o TEST)
+ - hatrac=$(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://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-hatrac-cli --host $dev.gudmap.org mkdir /hatrac/resources/rnaseq/pipeline/input_bag/TEST
+ 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=$(singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:Input_Bag/File_MD5=${md5})
+ - exist=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:Input_Bag/File_MD5=${md5})
- >
if [ "${exist}" == "[]" ]; then
cookie=$(cat credential.json | grep -A 1 '\"dev.gudmap.org\": {' | grep -o '\"cookie\": \".*\"')
cookie=${cookie:11:-1}
- loc=$(singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-hatrac-cli --host dev.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/input_bag/TEST/test.txt)
- inputBag_rid=$(singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' python3 uploadInputBag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -o dev.gudmap.org -c ${cookie})
+ loc=$(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)
+ inputBag_rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 uploadInputBag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -o dev.gudmap.org -c ${cookie})
fi
--
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