From 03d3816d56a94a180824792036f9eb830c6045f0 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 28 Dec 2020 15:28:38 -0600
Subject: [PATCH] Fix upload processed file ci unit
---
.gitlab-ci.yml | 7 +++----
1 file changed, 3 insertions(+), 4 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9344c87..c623e51 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -355,17 +355,16 @@ uploadProcessedFile:
- >
exist=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Processed_File/Replicate=17-BTFJ) &&
cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
- cookie=${cookie:11:-1}
+ cookie=${cookie:11:-1} &&
if [ "${exist}" != "[]" ]; then
rids=$(echo ${exist} | grep -o '\"RID\":\".\{7\}' | sed 's/^.\{7\}//') &&
for rid in ${rids}; do
singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/deleteEntry.py -r ${rid} -t Processed_File -o staging.gudmap.org -c ${cookie}
- echo old processed file RID deleted - ${rid}
done
echo all old processed file RIDs deleted
fi
- singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-upload-cli --catalog 2 --token ${cookie} staging.gudmap.org ./deriva
- - echo test processed file uploaded
+ singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-upload-cli --catalog 2 --token ${cookie} staging.gudmap.org ./deriva
+ echo test processed file uploaded
- mkdir test
- singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bdbag test --archiver zip
- echo test output bag created
--
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