diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 69d4f52abf88476cb906a789e42d7fa0827ff9a2..2a4894ab59125932860225e2ba06ffe77cf8135c 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -338,7 +338,7 @@ uploadQC: done echo all old mRNA QC RIDs deleted fi - rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadQC.py -r 17-BTFJ -e -p "Single Read" -s forward -l 35 -w 5 -f 1 -n 'This is a test mRNA QC' -o staging.gudmap.org -c ${cookie} -u F) && + rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadQC.py -r 17-BTFJ -e 17-BTG4 -p "Single Read" -s forward -l 35 -w 5 -f 1 -n 'This is a test mRNA QC' -o staging.gudmap.org -c ${cookie} -u F) && echo ${rid} test mRNA QC created uploadProcessedFile: @@ -351,8 +351,8 @@ uploadProcessedFile: script: - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json - echo THIS IS A TEST FILE > 17-BTFJ_test.csv - - mkdir -p ./deriva/Seq/pipeline/17-BTFA// - - mv 17-BTFJ_test.csv ./deriva/Seq/pipeline/17-BTFA//17-BTFJ_test.csv + - mkdir -p ./deriva/Seq/pipeline/17-BTFA/17-BTG4/ + - mv 17-BTFJ_test.csv ./deriva/Seq/pipeline/17-BTFA/17-BTG4/17-BTFJ_test.csv - > exist=$(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=$(cat credential.json | grep -A 1 '"staging.gudmap.org\: {' | grep -o '"cookie": ".*"') && @@ -390,7 +390,7 @@ uploadOutputBag: cookie=$(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 staging.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/output_bag/TEST/test.txt --parents) && - rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadOutputBag.py -e 18-MJ3C -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test output bag' -o staging.gudmap.org -c ${cookie}) && + rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadOutputBag.py -e 17-BTG4 -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test output bag' -o staging.gudmap.org -c ${cookie}) && echo ${rid} test output bag created else rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&