Update ref unit test for datahub

.gitlab-ci.yml

@@ -240,10 +240,12 @@ humanDataHub:
   - 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)
-  - refMD5=$(python ./workflow/scripts/extractRefData.py --returnParam MD5)
-  - test=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls /hatrac/resources/rnaseq/pipeline/reference_genome/)
-  - test=$(echo ${test} | grep -o ${refMD5})
-  - if [ "${test}" == "" ]; then exit 1; fi
+  - 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
 
 mousenDataHub:
   stage: reference
@@ -264,10 +266,12 @@ mousenDataHub:
   - 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)
-  - refMD5=$(python ./workflow/scripts/extractRefData.py --returnParam MD5)
-  - test=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls /hatrac/resources/rnaseq/pipeline/reference_genome/)
-  - test=$(echo ${test} | grep -o ${refMD5})
-  - if [ "${test}" == "" ]; then exit 1; fi
+  - 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: