.gitlab-ci.yml

stages:
  - test
  - deploy

variables:
  VCF_VALIDATOR_VERSION: 0.9.4
  MONGO_HOST: mongo
  POSTGRES_HOST: postgres
  POSTGRES_DB: postgres
  POSTGRES_USER: postgres
  POSTGRES_PASSWORD: postgres

test:
  stage: test
  image: ubuntu:20.04
  services:
    - mongo:4.0.21
    - postgres:9.6
  before_script:
    - apt-get update
    - apt-get upgrade -y
    - apt-get install -y tzdata
    - apt-get install -y wget
    - apt-get install -y curl
    - apt-get install -y git
    - apt-get install -y rsync
    - apt-get install -y openjdk-11-jdk
    - apt-get -y install maven samtools bcftools parallel libbz2-dev liblzma-dev
    - bash -c "export JAVA_CMD="$(which java)" && cd /usr/bin && (curl -s https://get.nextflow.io | bash) && chmod 755 nextflow"
    - /usr/bin/nextflow -version
    - bash -c "cd /usr/bin && wget https://github.com/EBIvariation/vcf-validator/releases/download/v$VCF_VALIDATOR_VERSION/vcf_validator_linux && chmod 755 vcf_validator_linux"
    - bash -c "cd /usr/bin && wget https://github.com/EBIvariation/vcf-validator/releases/download/v$VCF_VALIDATOR_VERSION/vcf_assembly_checker_linux && chmod 755 vcf_assembly_checker_linux"
    - apt-get install -y python3
    - apt-get install -y python3-pip
    - python3 -m pip install --upgrade pip
    - pip install pytest certifi
    - if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
    - python3 setup.py install
    - curl https://d3gcli72yxqn2z.cloudfront.net/connect_latest/v4/bin/ibm-aspera-connect_4.1.3.93_linux.tar.gz -o ibm-aspera-connect.tar.gz
    - tar xzf ibm-aspera-connect.tar.gz
    - ./ibm-aspera-connect_*_linux.sh
    - chmod +x ~/.aspera/connect/bin/ascp; ln -s ~/.aspera/connect/bin/ascp /usr/bin
    # reduce the default SSL security level to get around a misconfiguration in the Ensembl server
    # https://github.com/Ensembl/ensembl-rest/issues/427
    # See https://askubuntu.com/a/1233456
    - sed -i 's/DEFAULT@SECLEVEL=2/DEFAULT@SECLEVEL=1/' /usr/lib/ssl/openssl.cnf
    - export ASPERA_ID_DSA=~/.aspera/connect/etc/asperaweb_id_dsa.openssh
    - export NXF_DEFAULT_DSL=1
  script:
    - PYTHONPATH=. pytest tests
  environment:
    name: test-env
  only:
    - external_pull_requests
    - tags
    - master
    - main


# Not executed, parent job definition
.deploy-python-tool:
  stage: deploy
  image: ubuntu:20.04
  environment:
    name: $ENVIRONMENT_NAME
  script:
    # Start ssh-agent and set identity then copy the Jar file and create a symlink
    # See https://docs.gitlab.com/ee/ci/ssh_keys/
    - apt-get update
    - apt-get -y install openssh-client
    - eval "$(ssh-agent)"
    - echo "$EVA_ETL_PRIVATE_KEY" | tr -d '\r' | ssh-add -
    - ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null ${CLUSTER_USER}@${CLUSTER_LOGIN_NODE_CODON} "${EVA_SOFTWARE_PATH_CODON}/covid19dp-submission/${ENVIRONMENT_NAME}_deployments/deploy.sh ${DEPLOY_POINT}"
  dependencies:
    - test

deploy-python-tool-development:
  extends: .deploy-python-tool
  variables:
    ENVIRONMENT_NAME: development
    DEPLOY_POINT: $CI_COMMIT_BRANCH
  only:
    - external_pull_requests
    - master
    - main

deploy-python-tool-production:
  extends: .deploy-python-tool
  variables:
    ENVIRONMENT_NAME: production
    DEPLOY_POINT: $CI_COMMIT_TAG
  only:
    - tags