.gitlab-ci.yml

before_script:
  - module load python/3.6.4-anaconda
  - pip install --user attrs==20.3.0 pytest==6.2.2 pytest-pythonpath==0.7.3 pytest-cov==2.11.1
  - 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.vM25"
  refHuVersion: "38.p13.v36"
  refERCCVersion: "92"

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

build_badges:
  stage: badges
  only:
    - master
    - develop
    - tags
  before_script:
    - module load singularity/3.5.3
    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/
    - chmod +x ./workflow/scripts/get_updated_badge_info.sh
  script:
    - echo "Building badges"
    - singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' bash ./workflow/scripts/get_updated_badge_info.sh
    - singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' bash ./workflow/scripts/get_updated_rep_count.sh
  artifacts:
    paths:
      - badges/

pages:
  stage: deploy
  only:
    - master
    - develop
    - tags
  dependencies:
    - build_badges
  script:
    - mkdir -p public
    - mv badges/ public/badges/
  artifacts:
    paths:
    - public

getBag:
  stage: unit
  only:
    - push
    - tags
  except:
    - merge_requests
    - schedules
  script:
    - ln -sfn `readlink -e ./test_data/auth/credential.json` ~/.deriva/credential.json
    - singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-download-cli --version > version_deriva.txt
    - singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-download-cli staging.gudmap.org --catalog 2 ./workflow/conf/Replicate_For_Input_Bag.json . rid=Q-Y5F6
    - pytest -m getBag
  artifacts: