From 17df0fa5ed68da1834c812e03b9b3c5fea56ab5c Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sat, 12 Sep 2020 11:46:27 -0500
Subject: [PATCH] Fix extractRefData arg

---
 .gitlab-ci.yml                     | 8 ++++----
 workflow/scripts/extractRefData.py | 6 +++---
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 1fb4b3d..a8f136b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -239,8 +239,8 @@ humanDataHub:
   - 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 --return URL)
-  - refMD5=$(python ./workflow/scripts/extractRefData.py --return MD5)
+  - refURL=$(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/ | grep -o ${refMD5})
   - if [ "${test}" == "" ]; then exit 1; fi
 
@@ -262,8 +262,8 @@ mousenDataHub:
   - 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 --return URL)
-  - refMD5=$(python ./workflow/scripts/extractRefData.py --return MD5)
+  - refURL=$(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/ | grep -o ${refMD5})
   - if [ "${test}" == "" ]; then exit 1; fi
 
diff --git a/workflow/scripts/extractRefData.py b/workflow/scripts/extractRefData.py
index 8f58751..4e69b93 100644
--- a/workflow/scripts/extractRefData.py
+++ b/workflow/scripts/extractRefData.py
@@ -7,7 +7,7 @@ warnings.simplefilter(action='ignore', category=FutureWarning)
 
 def get_args():
     parser = argparse.ArgumentParser()
-    parser.add_argument('-r', '--return',help="The parameter to return (URL or MD5).",required=True)
+    parser.add_argument('-r', '--returnParam',help="The parameter to return (URL or MD5).",required=True)
     args = parser.parse_args()
     return args
 
@@ -15,9 +15,9 @@ def main():
     args = get_args()
     refQuery=pd.read_json("refQuery.json")
     if refQuery["File_URL"].count() == 1:
-        if args.return == "URL":
+        if args.returnParam == "URL":
             print(refQuery["File_URL"].values[0])
-        elif args.return == "MD5":
+        elif args.returnParam == "":
             print(refQuery["File_MD5"].values[0])
     else:
         raise Exception("Multple references found: \n%s" %
-- 
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