diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 086dafc12410ea34ce9576ec521e4c8f9487f1b1..8dda5a7c45d11161198fb2a3fb5986b16ba6b86e 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -289,19 +289,27 @@ uploadInputBag: - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json - > hatrac=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org ls /hatrac/resources/rnaseq/pipeline/input_bag/ | grep -o /TESTX$) - echo ${hatrac} && - if [ -z "${hatrac}" ]; then singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org mkdir /hatrac/resources/rnaseq/pipeline/input_bag/TESTX; fi + if [ -z "${hatrac}" ]; then + singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org mkdir /hatrac/resources/rnaseq/pipeline/input_bag/TEST + echo /hatrac/resources/rnaseq/pipeline/input_bag/TEST created + else + echo /hatrac/resources/rnaseq/pipeline/input_bag/TEST already exists + fi - echo THIS IS A TEST FILE > test.txt - > md5=$(md5sum ./test.txt | awk '{ print $1 }') && size=$(wc -c < ./test.txt) && - exist=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' curl -s https://dev.gudmap.org/ermrest/catalog/2/entity/RNASeq:Input_Bag/File_MD5=${md5}) && - echo $exist && + exist=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' curl -s https://dev.gudmap.org/ermrest/catalog/2/entity/RNASeq:Input_Bag/File_MD5=${md5}) if [ "${exist}" == "[]" ]; then cookie=$(cat credential.json | grep -A 1 '\"dev.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') && cookie=${cookie:11:-1} && loc=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/input_bag/TEST/test.txt) && - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadInputBag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -o dev.gudmap.org -c ${cookie} + rid=singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadInputBag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -o dev.gudmap.org -c ${cookie} && + echo ${rid} test input bag created + else + rid=\$(echo \${exist} | grep -o '\\"RID\\":\\".*\\",\\"RCT') && + rid=\${rid:8:-6} && + echo ${rid} test input bag already exists fi