.gitlab-ci.yml

image: maven:3.3.9-jdk-8-alpine

deploy:
  environment: prod
  before_script:
    - apk add --update openssh-client bash openssl rsync gettext tzdata
    - eval $(ssh-agent -s)
    - mkdir ~/.ssh
    - chmod 700 ~/.ssh
    - echo $SSH_KEY | base64 -d | tr -d '\r' | ssh-add - > /dev/null
    - DEPLOY_SERVERS_ARRAY=(`echo $DEPLOY_SERVER | tr ',' ' '`)
    - for i in "${DEPLOY_SERVERS_ARRAY[@]}"; do ssh-keyscan $i >> ~/.ssh/known_hosts; chmod 600 ~/.ssh/*; done
  script:
    - DEPLOY_DIR=$(date +"%Y%m%d_%H%M%S")
    - mkdir $DEPLOY_DIR

    # Substitute environment variables
    - envsubst < .params.config > params.config
    - envsubst '${PIPELINE_BASE_DIR},${LOG_FOLDER},${DATA_ROOT_DIR},${API_ENDPOINT_FILE_DOWNLOADS_PER_PROJECT},${API_ENDPOINT_FILE_DOWNLOADS_PER_FILE},${API_ENDPOINT_HEADER}' < scripts/.run_stat.sh > scripts/run_stat.sh
    - envsubst '${CONDA_INIT},${LOGS_SOURCE_ROOT},${LOGS_DESTINATION_ROOT},${PROFILE},${RESOURCE}' < .run_file_download_stats.sh > run_file_download_stats.sh

    # Move all necessary files to the deployment directory
    - rsync -a scripts *.config *.yml *.nf *.sh filedownloadstat conf params template "$DEPLOY_DIR/"

    # Secure permissions
    - cd $DEPLOY_DIR && chmod 755 *.sh scripts/* && cd ..

    # Deploy to HPC
    - ssh $SERVER_USER@$DEPLOY_SERVER "bash && mkdir -p $DEPLOY_PATH"
    - rsync -a $DEPLOY_DIR $SERVER_USER@$DEPLOY_SERVER:$DEPLOY_PATH/
    - ssh $SERVER_USER@$DEPLOY_SERVER "bash && cd $DEPLOY_PATH && ln -snf $DEPLOY_DIR $SYMLINK"
  when: manual
  allow_failure: false