From 686d27d4b99dd9941cabece0696f40dfcf12b818 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 28 Dec 2020 15:17:56 -0600
Subject: [PATCH] Use the correct docker container for upload processed files
ci unit
---
.gitlab-ci.yml | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index aee44f9..37a3cdf 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -355,7 +355,7 @@ 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
@@ -364,10 +364,10 @@ uploadProcessedFile:
done
echo all old processed file RIDs deleted
fi
- - singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' 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://bicf/gudmaprbkfilexfer:2.0.1_indev' bdbag test --archiver zip
+ - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bdbag test --archiver zip
- echo test output bag created
- pytest -m outputBag
--
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