diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 2c449ba3a9587d9f2dbed941b391b33c219d9a5b..2b088426351c84417bc5ff0f3787fe8409de630a 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -509,7 +509,7 @@ uploadProcessedFile: - 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}_${derivaVar}.sif curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Processed_File/Replicate=${ci_staging_rid_test_study}) && + 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_rep}) && cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') && cookie=${cookie:11:-1} && if [ "${exist}" != "[]" ]; then