.gitlab-ci.yml

image: quay.io/ucsc_cgl/toil_ci_prebake:latest
# Note that we must run in a privileged container for our internal Docker daemon to come up.

variables:
  PYTHONIOENCODING: "utf-8"
  DEBIAN_FRONTEND: "noninteractive"
  TOIL_OWNER_TAG: "shared"
  MAIN_PYTHON_PKG: "python3.11"
  TEST_THREADS: "3"
before_script:
  # Configure Docker to use a mirror for Docker Hub and restart the daemon
  # Set the registry as insecure because it is probably cluster-internal over plain HTTP.
  - |
    if [[ ! -z "${DOCKER_HUB_MIRROR}" ]] ; then
        echo "{\"registry-mirrors\": [\"${DOCKER_HUB_MIRROR}\"], \"insecure-registries\": [\"${DOCKER_HUB_MIRROR##*://}\"]}" | sudo tee /etc/docker/daemon.json
    fi
  # Restart or start the Docker daemon
  - stopdocker || true
  - sudo rm -f /var/run/docker.sock
  - startdocker || true
  - docker info
  - mkdir -p ~/.aws && cp "$GITLAB_SECRET_FILE_AWS_CREDENTIALS" ~/.aws/credentials

after_script:
  # We need to clean up any files that Toil may have made via Docker that
  # aren't deletable by the Gitlab user. If we don't do this, Gitlab will try
  # and clean them up before running the next job on the runner, fail, and fail
  # that next job.
  - pwd
  - sudo rm -rf tmp
  - stopdocker || true

stages:
  - main_tests


batch_systems:
  stage: main_tests
  script:
    - pwd
    - ${MAIN_PYTHON_PKG} -m virtualenv venv && . venv/bin/activate && pip install -U pip wheel && pip install .
    - wget https://github.com/ohsu-comp-bio/funnel/releases/download/0.10.1/funnel-linux-amd64-0.10.1.tar.gz
    - tar -xvf funnel-linux-amd64-0.10.1.tar.gz funnel
    - export FUNNEL_SERVER_USER=toil
    - export FUNNEL_SERVER_PASSWORD=$(openssl rand -hex 256)
    - |
      cat >funnel.conf <<EOF
      Server:
        BasicAuth:
          - User: ${FUNNEL_SERVER_USER}
            Password: ${FUNNEL_SERVER_PASSWORD}
      RPCClient:
        User: ${FUNNEL_SERVER_USER}
        Password: ${FUNNEL_SERVER_PASSWORD}
      LocalStorage:
        AllowedDirs:
          - $HOME/.aws
          - ./
      Compute: manual
      EOF
    - ./funnel server run -c funnel.conf &
    - ./funnel node run -c funnel.conf &
    - export TOIL_TES_ENDPOINT="http://127.0.0.1:8000"
    - export TOIL_TES_USER="${FUNNEL_SERVER_USER}"
    - export TOIL_TES_PASSWORD="${FUNNEL_SERVER_PASSWORD}"
    - ${MAIN_PYTHON_PKG} -m pytest --timeout=60 --log-level DEBUG --log-cli-level INFO src/toil_batch_system_tes/test/test.py
    - kill $(jobs -p) || true