.gitlab-ci.yml

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/

stages:
  - unit

unit:
  stage: unit
  script:
  - singularity run 'docker://bicf/bdbag:1.0' bdbag --materialize ./test_data/File_Q-Y53P.zip
  - singularity run 'docker://bicf/bdbag:1.0' bdbag --validate full ./test_data/File_Q-Y53P/
  - singularity run 'docker://bicf/bdbag:1.0' bdbag --validate completeness ./test_data/File_Q-Y53P/
  - find ./test_data/File_Q-Y53P/ -type f -print0 | xargs -0 md5sum > test.md5
  - md5sum -c test.md5
  - 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