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Commit c8efb567 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Fix CI unit uploadInputBag

parent 0f289056
2 merge requests!58Develop,!53Resolve "process_derivaUpload"
Pipeline #8422 failed with stages
in 1 minute and 32 seconds
......@@ -287,16 +287,16 @@ uploadInputBag:
- merge_requests
script:
- ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
- hatrac=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org ls /hatrac/resources/rnaseq/pipeline/input_bag/ | grep -o /TEST$)
- >
hatrac=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org ls /hatrac/resources/rnaseq/pipeline/input_bag/ | grep -o /TEST$) &&
if [ -z "${hatrac}" ]; then
singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org mkdir /hatrac/resources/rnaseq/pipeline/input_bag/TEST
fi
- echo THIS IS A TEST FILE > test.txt
- md5=$(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})
- >
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})
if [ "${exist}" == "[]" ]; then
cookie=$(cat credential.json | grep -A 1 '\"dev.gudmap.org\": {' | grep -o '\"cookie\": \".*\"')
cookie=${cookie:11:-1}
......
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