diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index aee44f9a5ca0c1d2348eea938765b89f04fc4c7d..37a3cdfeb12dc48378362c4f5eaa61147b432fb2 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -355,7 +355,7 @@ uploadProcessedFile: - > exist=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Processed_File/Replicate=17-BTFJ) && cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') && - cookie=${cookie:11:-1} && + cookie=${cookie:11:-1} if [ "${exist}" != "[]" ]; then rids=$(echo ${exist} | grep -o '\"RID\":\".\{7\}' | sed 's/^.\{7\}//') for rid in ${rids}; do @@ -364,10 +364,10 @@ uploadProcessedFile: done echo all old processed file RIDs deleted fi - - singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-upload-cli --catalog 2 --token ${cookie} staging.gudmap.org ./deriva + - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-upload-cli --catalog 2 --token ${cookie} staging.gudmap.org ./deriva - echo test processed file uploaded - mkdir test - - singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' bdbag test --archiver zip + - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bdbag test --archiver zip - echo test output bag created - pytest -m outputBag