diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index f591e8194b1ed954d047dfbc2abbba35a74ea76f..4e8858b312e2af1a97eb9ce7ba9fb105f4e0a650 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -283,7 +283,7 @@ uploadInputBag: size=$(wc -c < ./test.txt) && exist=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Input_Bag/File_MD5=${md5}) && if [ "${exist}" == "[]" ]; then - cookie=$(cat credential.json | grep -A 1 '\"dev.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') && + cookie=$(cat credential.json | grep -A 1 '\"staging.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 --parents) && rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadInputBag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test input bag' -o dev.gudmap.org -c ${cookie}) && @@ -305,7 +305,7 @@ uploadExecutionRun: - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json - > exist=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' curl -s https://dev.gudmap.org/ermrest/catalog/2/entity/RNASeq:Execution_Run/Workflow=18-DT5T/Reference_Genome=17-BPD4/Input_Bag=18-MHWC/Replicate=18-MJ3A) && - cookie=$(cat credential.json | grep -A 1 '\"dev.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') && + cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') && cookie=${cookie:11:-1} && if [ "${exist}" == "[]" ]; then rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadExecutionRun.py -r 18-MJ3A -w 18-DT5T -g 17-BPD4 -i 18-MHWC -s Success -d 'This is a test execution run' -o dev.gudmap.org -c ${cookie} -u F) &&