diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 1181343f1bb3f9085eacb57fabe343921489bf98..dc43b74e9b89674529ebf8c61e866b546125b3da 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -2,15 +2,13 @@ before_script: - module add python/3.6.1-2-anaconda - pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1 - module load singularity/3.0.2 - - ln -sfn /project/BICF/BICF_Core/shared/gudmap/cookies/deriva-cookies.txt ./test_data/ - - ln -sfn /project/BICF/BICF_Core/shared/gudmap/test_data/File_Q-Y53P.zip ./test_data/ + - ln -sfn /project/BICF/BICF_Core/shared/gudmap/test_data/ ./test_data/ stages: - unit -unit: +getBag: stage: unit script: - - singularity run 'docker://bicf/gudmaprbkfilexfer:1.1' bdbag --materialize ./test_data/File_Q-Y53P.zip - - singularity run 'docker://bicf/gudmaprbkfilexfer:1.1' bdbag --validate full ./test_data/File_Q-Y53P/ - - if [[ $(md5sum test_data/File_Q-Y53P/data/assets/Study/Q-Y4H0/Experiment/Q-Y4BY/Replicate/Q-Y5F8/hMARIS_SIX2+_RiboDep#1.gene.rpkm.txt | awk '{ print $1 }') != $(cat test_data/File_Q-Y53P/data/File.csv | cut -d ',' -f10 | tail -1) ]]; then exit 21; fi; + - ln -sf `readlink -e ./test_data/auth/credential.json` ~/.deriva/credential.json + - singularity run 'docker://bicf/gudmaprbkfilexfer:1.1' deriva-download-cli dev.gudmap.org --catalog 2 ./workflow/conf/replicate_export_config.json . rid=16-1ZX4 \ No newline at end of file