diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 0a25a449ba1030f3dd68e367f7e8f482f9f54ea2..990d92e7751a80042d967b5c8b6a2b34e0afc1c2 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -288,20 +288,22 @@ uploadInputBag: 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=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org ls /hatrac/resources/rnaseq/pipeline/input_bag/ | grep -o /TESTX$) && + echo ${hatrac} && if [ -z "${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 + singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org mkdir /hatrac/resources/rnaseq/pipeline/input_bag/TESTX && 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}) && + echo $exist && if [ "${exist}" == "[]" ]; then - cookie=$(cat credential.json | grep -A 1 '\"dev.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') - cookie=${cookie:11:-1} - loc=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/input_bag/TEST/test.txt) - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 uploadInputBag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -o dev.gudmap.org -c ${cookie} + cookie=$(cat credential.json | grep -A 1 '\"dev.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') && + cookie=${cookie:11:-1} && + loc=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/input_bag/TEST/test.txt) && + singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 uploadInputBag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -o dev.gudmap.org -c ${cookie} && fi