From 9fa62f015acca656049e6a7b5fef590b01f8f0b3 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 30 Nov 2020 17:02:54 -0600
Subject: [PATCH] Finalize CI unit uploadInputBag
---
.gitlab-ci.yml | 18 +++++++++++++-----
1 file changed, 13 insertions(+), 5 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 086dafc..8dda5a7 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -289,19 +289,27 @@ uploadInputBag:
- ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
- >
hatrac=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org ls /hatrac/resources/rnaseq/pipeline/input_bag/ | grep -o /TESTX$)
- echo ${hatrac} &&
- if [ -z "${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/TESTX; fi
+ if [ -z "${hatrac}" ]; then
+ singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org mkdir /hatrac/resources/rnaseq/pipeline/input_bag/TEST
+ echo /hatrac/resources/rnaseq/pipeline/input_bag/TEST created
+ else
+ echo /hatrac/resources/rnaseq/pipeline/input_bag/TEST already exists
+ fi
- echo THIS IS A TEST FILE > test.txt
- >
md5=$(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}) &&
- echo $exist &&
+ exist=$(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} &&
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) &&
- 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') &&
+ rid=\${rid:8:-6} &&
+ echo ${rid} test input bag already exists
fi
--
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