.gitlab-ci.yml

before_script:
  - module add  python/3.6.4-anaconda
  - pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1
  - 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

stages:
  - unit
  - 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://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-download-cli dev.gudmap.org --catalog 2 ./workflow/conf/replicate_export_config.json . rid=Q-Y5F6
  - pytest -m getBag

getData:
  stage: unit
  only:
    - push
    - tags
  except:
    - merge_requests
  script:
  - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
  - unzip ./test_data/bag/Replicate_Q-Y5F6.zip
  - singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' bash ./workflow/scripts/bdbagFetch.sh Replicate_Q-Y5F6 Replicate_Q-Y5F6 TEST
  - pytest -m getData

parseMetadata:
  stage: unit
  only:
    - push
    - tags
  except:
    - merge_requests
  script:
  - rep=$(singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p repRID)
  - exp=$(singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p expRID)
  - study=$(singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p studyRID)
  - endsMeta=$(singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsMeta)
  - endsManual=$(singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsManual)
  - stranded=$(singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p stranded)
  - spike=$(singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p spike)
  - species=$(singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p species)
  - readLength=$(singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.stageNew.csv" -p readLength)
  - echo -e "${endsMeta},${endsManual},${stranded},${spike},${species},${readLength},${exp},${study},${rep}" > design.csv
  - pytest -m parseMetadata

inferMetadata:
  stage: unit
  only:
    - push
    - tags
  except:
    - merge_requests
  script:
  - >
    align=$(echo $(grep "Overall alignment rate" ./test_data/meta/Q-Y5F6_1M.se.alignSummary.txt | cut -f2 -d ':' | cut -f2 -d ' ' | tr -d '%')) &&
    if [[ ${align} == "" ]]; then exit 1; fi