From e618a23f538e4d86fc43babab0ce5b5739e0c2f0 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 28 Dec 2020 15:22:10 -0600
Subject: [PATCH] Fix upload processed file ci unit
---
.gitlab-ci.yml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 37a3cdf..1278486 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -357,14 +357,14 @@ uploadProcessedFile:
cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
cookie=${cookie:11:-1}
if [ "${exist}" != "[]" ]; then
- rids=$(echo ${exist} | grep -o '\"RID\":\".\{7\}' | sed 's/^.\{7\}//')
+ rids=$(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
+ 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
--
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