diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index b2eae12f30ee36dbaccfda73484bf3f5f1ed9f8d..eb96c17b5924f52d3b2d2eed2b82fd211a4a2678 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -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}