diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 190720465d7970c78b95d41fd52717619ac289b3..aba54e75f30c1367626cfa219d0a9dc574c8a27b 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -287,21 +287,21 @@ uploadInputBag: - merge_requests script: - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json - - hatrac=$(singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-hatrac-cli --host dev.gudmap.org ls /hatrac/resources/rnaseq/pipeline/input_bag/ | grep -o TEST) + - hatrac=$(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://bicf/gudmaprbkfilexfer:2.0.1_indev' 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 $dev.gudmap.org mkdir /hatrac/resources/rnaseq/pipeline/input_bag/TEST fi - echo THIS IS A TEST FILE > test.txt - md5=$(md5sum ./test.txt | awk '{ print $1 }') - size=$(wc -c < ./test.txt) - - exist=$(singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:Input_Bag/File_MD5=${md5}) + - exist=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:Input_Bag/File_MD5=${md5}) - > if [ "${exist}" == "[]" ]; then cookie=$(cat credential.json | grep -A 1 '\"dev.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') cookie=${cookie:11:-1} - loc=$(singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-hatrac-cli --host dev.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/input_bag/TEST/test.txt) - inputBag_rid=$(singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' python3 uploadInputBag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -o dev.gudmap.org -c ${cookie}) + loc=$(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) + inputBag_rid=$(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