diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 1e104e328859e2b22c38bcc379df6b1daba97103..63a773a70a31266f96bf54a1bdc61c2f8fc94098 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -240,10 +240,12 @@ humanDataHub: - 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) - - refMD5=$(python ./workflow/scripts/extractRefData.py --returnParam MD5) - - test=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls /hatrac/resources/rnaseq/pipeline/reference_genome/) - - test=$(echo ${test} | grep -o ${refMD5}) - - if [ "${test}" == "" ]; then exit 1; fi + - 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 mousenDataHub: stage: reference @@ -264,10 +266,12 @@ mousenDataHub: - 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) - - refMD5=$(python ./workflow/scripts/extractRefData.py --returnParam MD5) - - test=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls /hatrac/resources/rnaseq/pipeline/reference_genome/) - - test=$(echo ${test} | grep -o ${refMD5}) - - if [ "${test}" == "" ]; then exit 1; fi + - 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: