Fix extractRefData arg

.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
 

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" %