Add ref ci test for production

.gitlab-ci.yml

@@ -421,7 +421,7 @@ generateVersions:
     expire_in: 7 days
 
 
-humanBioHPC:
+human_BioHPC:
   stage: reference
   only:
     - push
@@ -432,7 +432,7 @@ humanBioHPC:
   - mkdir -p hu
   - cp -R /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2 ./hu/
 
-mouseBioHPC:
+mouse_BioHPC:
   stage: reference
   only:
     - push
@@ -443,7 +443,7 @@ mouseBioHPC:
   - mkdir -p mo
   - cp -R /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2 ./mo/
 
-humanDataHub_dev:
+human_dev.gudmap.org:
   stage: reference
   only:
     - push
@@ -468,7 +468,7 @@ humanDataHub_dev:
   - test=$(echo ${test} | grep -o ${filename})
   - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi
 
-mouseDataHub_dev:
+mouse_dev.gudmap.org:
   stage: reference
   only:
     - push
@@ -493,7 +493,7 @@ mouseDataHub_dev:
   - test=$(echo ${test} | grep -o ${filename})
   - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi
 
-humanDataHub_staging:
+human_staging.gudmap.org:
   stage: reference
   only:
     - push
@@ -518,7 +518,7 @@ humanDataHub_staging:
   - test=$(echo ${test} | grep -o ${filename})
   - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi
 
-mouseDataHub_staging:
+mouse_staging.gudmap.org:
   stage: reference
   only:
     - push
@@ -544,6 +544,58 @@ mouseDataHub_staging:
   - test=$(echo ${test} | grep -o ${filename})
   - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi
 
+human_www.gudmap.org:
+  stage: reference
+  only:
+    - push
+    - tags
+  except:
+    - merge_requests
+  script:
+  - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
+  - referenceBase=www.gudmap.org
+  - refName=GRCh
+  - references=$(echo ${referenceBase}/${refName}${refHuVersion})
+  - GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
+  - GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
+  - GENCODE=$(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)
+  - loc=$(dirname ${refURL})
+  - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
+  - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
+  - test=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
+  - test=$(echo ${test} | grep -o ${filename})
+  - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi
+
+mouse_www.gudmap.org:
+  stage: reference
+  only:
+    - push
+    - tags
+  except:
+    - merge_requests
+  script:
+  - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
+  - referenceBase=www.gudmap.org
+  - refName=GRCm
+  - refHuVersion=38.p6.vM22
+  - references=$(echo ${referenceBase}/${refName}${refHuVersion})
+  - GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
+  - GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
+  - GENCODE=$(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)
+  - loc=$(dirname ${refURL})
+  - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
+  - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
+  - test=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
+  - test=$(echo ${test} | grep -o ${filename})
+  - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi
+
+
 integration_se:
   stage: integration
   only: [merge_requests]