From 5a942ab64551f881c2d760894c96de056d4d363d Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 29 Dec 2020 15:41:03 -0600
Subject: [PATCH] Add fix last ' in ref ci

---
 .gitlab-ci.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 85cbff2..0a46ee0 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -458,7 +458,7 @@ human_dev:
   - 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})
+  - 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 ${refURL})
@@ -483,7 +483,7 @@ mouse_dev:
   - GRCv=$(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})
+  - 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 ${refURL})
@@ -508,7 +508,7 @@ human_staging:
   - GRCv=$(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})
+  - 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 ${refURL})
@@ -534,7 +534,7 @@ mouse_staging:
   - GRCv=$(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})
+  - 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 ${refURL})
@@ -559,7 +559,7 @@ human_prod:
   - GRCv=$(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})
+  - 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 ${refURL})
@@ -585,7 +585,7 @@ mouse_prod:
   - GRCv=$(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})
+  - 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})
-- 
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