diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 0c7f1c3628722b9df82ed443a79e23a455b6eb1d..1d953286f790ec9d0096c541ddbfa1301f94212b 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -604,7 +604,7 @@ human_dev: - curl --request GET ${query} > refQuery.json - refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL) - loc=$(dirname ${refURL}) - - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi + - if [ "${loc}" == "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)') - test=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif deriva-hatrac-cli --host ${referenceBase} ls ${loc}/) - test=$(echo ${test} | grep -o ${filename}) @@ -633,7 +633,7 @@ mouse_dev: - curl --request GET ${query} > refQuery.json - refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL) - loc=$(dirname ${refURL}) - - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi + - if [ "${loc}" == "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)') - test=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif deriva-hatrac-cli --host ${referenceBase} ls ${loc}/) - test=$(echo ${test} | grep -o ${filename}) @@ -662,7 +662,7 @@ human_staging: - curl --request GET ${query} > refQuery.json - refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL) - loc=$(dirname ${refURL}) - - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi + - if [ "${loc}" == "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)') - test=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif deriva-hatrac-cli --host ${referenceBase} ls ${loc}/) - test=$(echo ${test} | grep -o ${filename}) @@ -692,7 +692,7 @@ mouse_staging: - curl --request GET ${query} > refQuery.json - refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL) - loc=$(dirname ${refURL}) - - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi + - if [ "${loc}" == "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)') - test=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif deriva-hatrac-cli --host ${referenceBase} ls ${loc}/) - test=$(echo ${test} | grep -o ${filename}) @@ -721,7 +721,7 @@ human_prod: - curl --request GET ${query} > refQuery.json - refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL) - loc=$(dirname ${refURL}) - - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi + - if [ "${loc}" == "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)') - test=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif deriva-hatrac-cli --host ${referenceBase} ls ${loc}/) - test=$(echo ${test} | grep -o ${filename}) @@ -751,7 +751,7 @@ mouse_prod: - curl --request GET ${query} > refQuery.json - refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL) - loc=$(dirname ${refURL}) - - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi + - if [ "${loc}" == "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)') - test=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif deriva-hatrac-cli --host ${referenceBase} ls ${loc}/) - test=$(echo ${test} | grep -o ${filename}) @@ -1039,13 +1039,7 @@ dnanexus: jobID=$(cat dx.log | grep -oP "Job ID: \K.*") - dx watch ${jobID} --auth-token ${dnanexus_authToken} --project-context-id ${dnanexus_workspace} - status=$(dx find executions --id ${jobID} --state failed --brief --auth-token ${dnanexus_authToken} --project-context-id ${dnanexus_workspace}) - - > - if [ ${status} == "" ] - then - curl --request GET https://img.shields.io/badge/Envronment%3A%20DNAnexus-run%20succesful-success?style=flat > ./badges/env/dnanexus.svg - else - curl --request GET https://img.shields.io/badge/Envronment%3A%20DNAnexus-run%20failed-critical?style=flat > ./badges/env/dnanexus.svg - fi + - if [ ${status} == "" ]; then curl --request GET https://img.shields.io/badge/Envronment%3A%20DNAnexus-run%20succesful-success?style=flat > ./badges/env/dnanexus.svg; else curl --request GET https://img.shields.io/badge/Envronment%3A%20DNAnexus-run%20failed-critical?style=flat > ./badges/env/dnanexus.svg; fi after_script: - module load dxtoolkit/python27/0.294.0 - dx rm /ci-env/auth/* --all --auth-token ${dnanexus_authToken} --project-context-id ${dnanexus_workspace}