diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 92064327faad16709df16360105545d91aff9f98..2c449ba3a9587d9f2dbed941b391b33c219d9a5b 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -505,11 +505,11 @@ uploadProcessedFile: - derivaVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deriva | cut -d"/" -f2 | cut -d":" -f2) - echo ${dir}${derivaImg}_${derivaVar}.sif - 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-BTFE/17-BVDJ/ - - mv 17-BTFJ_test.csv ./deriva/Seq/pipeline/17-BTFE/17-BVDJ/17-BTFJ_test.csv + - echo THIS IS A TEST FILE > ${ci_staging_rid_test_rep}_test.csv + - mkdir -p ./deriva/Seq/pipeline/${ci_staging_rid_test_study}/${ci_staging_rid_test_erun}/ + - mv ${ci_staging_rid_test_rep}_test.csv ./deriva/Seq/pipeline/${ci_staging_rid_test_study}/${ci_staging_rid_test_erun}/${ci_staging_rid_test_rep}_test.csv - > - exist=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Processed_File/Replicate=17-BTFJ) && + exist=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Processed_File/Replicate=${ci_staging_rid_test_study}) && cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') && cookie=${cookie:11:-1} && if [ "${exist}" != "[]" ]; then