.gitlab-ci.yml

before_script:
  - module load python/3.6.4-anaconda
  - pip install --user  attrs==19.1.0 pytest-pythonpath==0.7.1 pytest-cov==2.5.1 deriva==1.3.0
  - module load singularity/3.5.3
  - module load nextflow/20.01.0
  - ln -sfn /project/BICF/BICF_Core/shared/gudmap/test_data/* ./test_data/
  - mkdir -p ~/.deriva
  - mkdir -p ~/.bdbag

variables:
  refMoVersion: "38.p6.vM22"
  refHuVersion: "38.p12.v31"
  refERCCVersion: "92"

stages:
  - unit
  - aggregation
  - reference
  - integration
  - consistency


getBag:
  stage: unit
  only:
    - push
    - tags
  except:
    - merge_requests
  script:
  - ln -sfn `readlink -e ./test_data/auth/credential.json` ~/.deriva/credential.json
  - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-download-cli --version > version_deriva.txt
  - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-download-cli staging.gudmap.org --catalog 2 ./workflow/conf/Replicate_For_Input_Bag.json . rid=Q-Y5F6
  - pytest -m getBag
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
    paths:
      - version_deriva.txt
    expire_in: 7 days

getData:
  stage: unit
  only:
    - push
    - tags
  except:
    - merge_requests
  script:
  - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bdbag --version > version_bdbag.txt
  - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
  - unzip ./test_data/bag/Q-Y5F6_inputBag.zip
  - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bash ./workflow/scripts/bdbagFetch.sh Q-Y5F6_inputBag Q-Y5F6 TEST
  - pytest -m getData
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
    paths:
      - version_bdbag.txt
    expire_in: 7 days

parseMetadata:
  stage: unit
  only:
    - push
    - tags
  except:
    - merge_requests
  script:
  - singularity run 'docker://gudmaprbk/python3:1.0.0' python3 --version > version_python.txt