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Commit b5af3a01 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Fix extract ref data python script name

parent 5a942ab6
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2 merge requests!58Develop,!53Resolve "process_derivaUpload"
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.gitlab-ci.yml
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......@@ -460,7 +460,7 @@ human_dev:
- 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)
- 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
- filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
......@@ -485,7 +485,7 @@ mouse_dev:
- GENCODE=$(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)
- 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
- filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
......@@ -510,7 +510,7 @@ human_staging:
- GENCODE=$(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)
- 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
- filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
......@@ -536,7 +536,7 @@ mouse_staging:
- GENCODE=$(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)
- 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
- filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
......@@ -561,7 +561,7 @@ human_prod:
- GENCODE=$(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)
- 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
- filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
......@@ -587,7 +587,7 @@ mouse_prod:
- GENCODE=$(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)
- 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
- filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
......
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