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Commit 00983e2b authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Fix CI lint

parent 97cd5936
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2 merge requests!58Develop,!45Resolve "Move references to GUDMAP/RBK"
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.gitlab-ci.yml
+ 23
− 23
View file @ 00983e2b
...@@ -9,7 +9,7 @@ before_script: ...@@ -9,7 +9,7 @@ before_script:
stages: stages:
- unit - unit
- references - reference
- integration - integration
- consistency - consistency
...@@ -229,17 +229,17 @@ humanDataHub: ...@@ -229,17 +229,17 @@ humanDataHub:
except: except:
- merge_requests - merge_requests
script: script:
referenceBase=dev.gudmap.org - referenceBase=dev.gudmap.org
refName=GRCh - refName=GRCh
refHuVersion=38.p12.v31 - refHuVersion=38.p12.v31
references=$(echo ${referenceBase}/${refName}${refHuVersion}) - references=$(echo ${referenceBase}/${refName}${refHuVersion})
GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1) - GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2) - GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3) - GENCODE=$(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}) - 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 - curl --request GET ${query} > refQuery.json
refURL=$(python ./workflow/scripts/extractRefData.py) - refURL=$(python ./workflow/scripts/extractRefData.py)
deriva-hatrac-cli --host ${referenceBase} get ${refURL} - singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-hatrac-cli --host ${referenceBase} get ${refURL}
mousenDataHub: mousenDataHub:
stage: reference stage: reference
...@@ -249,17 +249,17 @@ mousenDataHub: ...@@ -249,17 +249,17 @@ mousenDataHub:
except: except:
- merge_requests - merge_requests
script: script:
referenceBase=dev.gudmap.org - referenceBase=dev.gudmap.org
refName=GRCm - refName=GRCm
refHuVersion=38.p6.vM22 - refHuVersion=38.p6.vM22
references=$(echo ${referenceBase}/${refName}${refHuVersion}) - references=$(echo ${referenceBase}/${refName}${refHuVersion})
GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1) - GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2) - GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3) - GENCODE=$(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}) - 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 - curl --request GET ${query} > refQuery.json
refURL=$(python ./workflow/scripts/extractRefData.py) - refURL=$(python ./workflow/scripts/extractRefData.py)
deriva-hatrac-cli --host ${referenceBase} get ${refURL} - singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-hatrac-cli --host ${referenceBase} get ${refURL}
integration_se: integration_se:
......
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