diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 9344c873d84e02888b4ae8d199d41b3b957f6171..c623e51e8f2a39366b799d374d440ef49b8e7415 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -355,17 +355,16 @@ 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 singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/deleteEntry.py -r ${rid} -t Processed_File -o staging.gudmap.org -c ${cookie} - echo old processed file RID deleted - ${rid} done echo all old processed file RIDs deleted fi - 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 + 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://gudmaprbk/deriva1.3:1.0.0' bdbag test --archiver zip - echo test output bag created