From 45b7f6794cb4f2502ecf912eb81dcd6e2e56eb9a Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 13 Sep 2020 10:56:34 -0500
Subject: [PATCH] Update ref unit test for datahub
---
.gitlab-ci.yml | 20 ++++++++++++--------
1 file changed, 12 insertions(+), 8 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 1e104e3..63a773a 100644
--- a/.gitlab-ci.yml
+++ b/.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:
--
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