.travis.yml

sudo: required

language: python
python: 3.10

services:
  - docker

env:
  matrix:
    - TOX_ENV=py310
  global:
    - secure: "SEjcKJQ0NGXdpFxFhLVlyJmiBvgiLtR5Uufg90Vm3owKlMy0NSfIrOR+2dwNniqOp7QI3eVepnqjid/Ka0QStzVqMCe55OLkJ/TbTHnMLpbtY63mpGfogVRvxMMAVpzLpcQqtJFORZmO/MIWSLlBiXMMzOg3+tbXvQXmL17Rbmw="

matrix:
  allow_failures:
    - env: KUBE=True

git:
  submodules: false

before_install:
  - set -e
  - export GALAXY_HOME=/home/galaxy
  - export GALAXY_USER=admin@example.org
  - export GALAXY_USER_EMAIL=admin@example.org
  - export GALAXY_USER_PASSWD=password
  - export BIOBLEND_GALAXY_API_KEY=fakekey
  - export BIOBLEND_GALAXY_URL=http://localhost:8080

  - sudo apt-get update -qq
  - sudo apt-get install docker-ce --no-install-recommends -y -o Dpkg::Options::="--force-confmiss" -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confnew"
  - sudo apt-get install sshpass --no-install-recommends -y
  - pip install ephemeris

  - docker --version
  - docker info


  # start building this repo
  - sudo chown 1450 /tmp && sudo chmod a=rwx /tmp
  - export WORKING_DIR="$TRAVIS_BUILD_DIR"
  - export DOCKER_RUN_CONTAINER="quay.io/bgruening/galaxy"
  - export INSTALL_REPO_ARG=""
  - export SAMPLE_TOOLS=$GALAXY_HOME/ephemeris/sample_tool_list.yaml
  - travis_wait 30 cd "$WORKING_DIR" && docker build -t quay.io/bgruening/galaxy galaxy/
  - |
    ## define a container size check function, first parameter is the container name, second the max allowed size in MB
    container_size_check () {

        # check that the image size is not growing too much between releases
        # the 19.05 monolithic image was around 1.500 MB
        size=`docker image inspect $1 --format='{{.Size}}'`
        size_in_mb=$(($size/(1024*1024)))
        if [[ $size_in_mb -ge $2 ]]
        then
            echo "The new compiled image ($1) is larger than allowed. $size_in_mb vs. $2"
            sleep 2
            #exit
        fi
    }
    container_size_check   quay.io/bgruening/galaxy  1500

    mkdir local_folder
    docker run -d -p 8080:80 -p 8021:21 -p 8022:22 \
        --name galaxy \
        --privileged=true \
        -v `pwd`/local_folder:/export/ \
        -e GALAXY_CONFIG_ALLOW_USER_DATASET_PURGE=True \
        -e GALAXY_CONFIG_ALLOW_PATH_PASTE=True \
        -e GALAXY_CONFIG_ALLOW_USER_DELETION=True \
        -e GALAXY_CONFIG_ENABLE_BETA_WORKFLOW_MODULES=True \
        -v /tmp/:/tmp/ \
        quay.io/bgruening/galaxy

    sleep 30
    docker logs galaxy
    # Define start functions
    docker_exec() {
      cd $WORKING_DIR
      docker exec -t -i galaxy "$@"
    }
    docker_exec_run() {
      cd $WORKING_DIR
      docker run quay.io/bgruening/galaxy "$@"
    }
    docker_run() {
      cd $WORKING_DIR
      docker run "$@"
    }

  - docker ps

script:
  - set -e
  # Test submitting jobs to an external slurm cluster
  - cd $TRAVIS_BUILD_DIR/test/slurm/ && bash test.sh && cd $WORKING_DIR
  # Test submitting jobs to an external gridengine cluster
  # TODO 19.05, need to enable this again!
  # - cd $TRAVIS_BUILD_DIR/test/gridengine/ && bash test.sh && cd $WORKING_DIR

  - echo 'Waiting for Galaxy to come up.'
  - galaxy-wait -g $BIOBLEND_GALAXY_URL --timeout 600

  - curl -v --fail $BIOBLEND_GALAXY_URL/api/version

  # Test self-signed HTTPS
  - docker_run -d --name httpstest -p 443:443 -e "USE_HTTPS=True" $DOCKER_RUN_CONTAINER

  - sleep 180s && curl -v -k --fail https://127.0.0.1:443/api/version
  - echo | openssl s_client -connect 127.0.0.1:443 2>/dev/null | openssl x509 -issuer -noout| grep localhost

  - docker logs httpstest && docker stop httpstest && docker rm httpstest

  # Test FTP Server upload
  - date > time.txt && curl -v --fail -T time.txt ftp://localhost:8021 --user $GALAXY_USER:$GALAXY_USER_PASSWD || true
  # Test FTP Server get
  - curl -v --fail ftp://localhost:8021 --user $GALAXY_USER:$GALAXY_USER_PASSWD

  # Test CVMFS
  - docker_exec bash -c "service autofs start"
  - docker_exec bash -c "cvmfs_config chksetup"
  - docker_exec bash -c "ls /cvmfs/data.galaxyproject.org/byhand"

  # Test SFTP Server
  - sshpass -p $GALAXY_USER_PASSWD sftp -v -P 8022 -o User=$GALAXY_USER -o "StrictHostKeyChecking no" localhost <<< $'put time.txt'

  # Run a ton of BioBlend test against our servers.
  - cd $TRAVIS_BUILD_DIR/test/bioblend/ && . ./test.sh && cd $WORKING_DIR/

  # not working anymore in 18.01
  # executing: /galaxy_venv/bin/uwsgi --yaml /etc/galaxy/galaxy.yml --master --daemonize2 galaxy.log --pidfile2 galaxy.pid  --log-file=galaxy_install.log --pid-file=galaxy_install.pid
  # [uWSGI] getting YAML configuration from /etc/galaxy/galaxy.yml
  # /galaxy_venv/bin/python: unrecognized option '--log-file=galaxy_install.log'
  # getopt_long() error
  # cat: galaxy_install.pid: No such file or directory
  # tail: cannot open ‘galaxy_install.log’ for reading: No such file or directory
  #- |
  #  if [ "${COMPOSE_SLURM}" ] || [ "${KUBE}" ] || [ "${COMPOSE_CONDOR_DOCKER}" ] || [ "${COMPOSE_SLURM_SINGULARITY}" ]
  #  then
  #      # Test without install-repository wrapper
  #      sleep 10
  #      docker_exec_run bash -c 'cd $GALAXY_ROOT_DIR && python ./scripts/api/install_tool_shed_repositories.py --api admin -l http://localhost:80 --url https://toolshed.g2.bx.psu.edu -o devteam --name cut_columns --panel-section-name BEDTools'
  #  fi


  # Test the 'new' tool installation script
  - docker_exec install-tools "$SAMPLE_TOOLS"
  # Test the Conda installation
  - docker_exec_run bash -c 'export PATH=$GALAXY_CONFIG_TOOL_DEPENDENCY_DIR/_conda/bin/:$PATH && conda --version && conda install samtools -c bioconda --yes'


after_success:
  - |
    if [ "$TRAVIS_PULL_REQUEST" == "false" -a "$TRAVIS_BRANCH" == "master" ]
    then
        cd ${TRAVIS_BUILD_DIR}
        echo "Generate and deploy html documentation"
        ./docs/bin/deploy_docs
    fi


notifications:
  webhooks:
    urls:
      - https://webhooks.gitter.im/e/559f5480ac7a4ef238af
    on_success: change
    on_failure: always
    on_start: never