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" % -- GitLab