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Commit 686d27d4 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Use the correct docker container for upload processed files ci unit

parent 9da15a83
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2 merge requests!58Develop,!53Resolve "process_derivaUpload"
Pipeline #8613 canceled with stages
......@@ -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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