diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 195ac488bf9064f8143e023c5bb4c44a9a92c663..c99f520e33e62acc4dc88e8d7990f285d20db552 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -421,7 +421,7 @@ generateVersions: expire_in: 7 days -humanBioHPC: +human_BioHPC: stage: reference only: - push @@ -432,7 +432,7 @@ humanBioHPC: - mkdir -p hu - cp -R /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2 ./hu/ -mouseBioHPC: +mouse_BioHPC: stage: reference only: - push @@ -443,7 +443,7 @@ mouseBioHPC: - mkdir -p mo - cp -R /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2 ./mo/ -humanDataHub_dev: +human_dev.gudmap.org: stage: reference only: - push @@ -468,7 +468,7 @@ humanDataHub_dev: - test=$(echo ${test} | grep -o ${filename}) - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi -mouseDataHub_dev: +mouse_dev.gudmap.org: stage: reference only: - push @@ -493,7 +493,7 @@ mouseDataHub_dev: - test=$(echo ${test} | grep -o ${filename}) - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi -humanDataHub_staging: +human_staging.gudmap.org: stage: reference only: - push @@ -518,7 +518,7 @@ humanDataHub_staging: - test=$(echo ${test} | grep -o ${filename}) - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi -mouseDataHub_staging: +mouse_staging.gudmap.org: stage: reference only: - push @@ -544,6 +544,58 @@ mouseDataHub_staging: - test=$(echo ${test} | grep -o ${filename}) - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi +human_www.gudmap.org: + stage: reference + only: + - push + - tags + except: + - merge_requests + script: + - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt + - referenceBase=www.gudmap.org + - refName=GRCh + - references=$(echo ${referenceBase}/${refName}${refHuVersion}) + - GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1) + - GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2) + - GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3) + - query=$(echo 'https://'${referenceBase}'/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='${GRCv}'.'${GRCp}'/Annotation_Version=GENCODE%20'${GENCODE}) + - curl --request GET ${query} > refQuery.json + - refURL=$(python ./workflow/scripts/extractRefData.py --returnParam URL) + - loc=$(dirname ${refURL}) + - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi + - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)') + - test=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/) + - test=$(echo ${test} | grep -o ${filename}) + - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi + +mouse_www.gudmap.org: + stage: reference + only: + - push + - tags + except: + - merge_requests + script: + - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt + - referenceBase=www.gudmap.org + - refName=GRCm + - refHuVersion=38.p6.vM22 + - references=$(echo ${referenceBase}/${refName}${refHuVersion}) + - GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1) + - GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2) + - GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3) + - query=$(echo 'https://'${referenceBase}'/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='${GRCv}'.'${GRCp}'/Annotation_Version=GENCODE%20'${GENCODE}) + - curl --request GET ${query} > refQuery.json + - refURL=$(python ./workflow/scripts/extractRefData.py --returnParam URL) + - loc=$(dirname ${refURL}) + - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi + - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)') + - test=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/) + - test=$(echo ${test} | grep -o ${filename}) + - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi + + integration_se: stage: integration only: [merge_requests]