.gitlab-ci.yml

default:
    image: python:3.7

variables:
    MONGO_HOST: "localhost"
    MONGO_PORT: 27017
    MONGO_USERNAME: ""
    MONGO_PASSWORD: ""
    MONGO_DBNAME: matchminer_test
    MONGO_URI: mongodb://localhost:27017/matchminer_test
    ONCOTREE_CUSTOM_DIR: /builds/matchminer/matchminerAPI/data/oncotree_file.txt
    EMAIL_CONFIG: /builds/matchminer/matchminerAPI/email.config.json
    SECRETS_JSON: /builds/matchminer/matchminerAPI/SECRETS_JSON.json

before_script:
    # install mongo
    - apt-get update && apt install -y dirmngr gnupg apt-transport-https software-properties-common ca-certificates curl
    - wget -qO - https://www.mongodb.org/static/pgp/server-4.2.asc | apt-key add -
    - add-apt-repository 'deb https://repo.mongodb.org/apt/debian buster/mongodb-org/4.2 main'
    - apt-get update
    - apt-get install -y mongodb-org libxml2-dev libxslt1-dev libxmlsec1-dev
    - DEBIAN_FRONTEND=noninteractive apt-get update --fix-missing && apt-get update
    - mkdir -p /data/db && touch mongod.log
    - mongod --logpath /builds/matchminer/matchminerAPI/mongod.log --quiet &

    # load test data
    - mongorestore -d matchminer_test --dir=tests/data
    - pip install -r requirements.txt

    # set secrets file and run tests
    - echo "{\"MONGO_HOST\":\"$MONGO_HOST\",\"MONGO_PORT\":\"$MONGO_PORT\",\"MONGO_USERNAME\":\"$MONGO_USERNAME\",\"MONGO_PASSWORD\":\"$MONGO_PASSWORD\",\"MONGO_DBNAME\":\"$MONGO_DBNAME\",\"MONGO_URI\":\"$MONGO_URI\"}" > SECRETS_JSON.json

run_test:
  script:
    - nosetests -v tests/unit
    - nosetests -v --with-xunit --with-coverage tests


  artifacts:
    reports:
      junit: nosetests.xml