.travis.yml

dist: trusty
language: python
language: node_js
node_js:
  - "12"
# qiita travis has set sudo to false
sudo: required
#addons:
  # install chrome for testing purposes
  #  chrome: stable
group: deprecated-2017Q4
env:
  - PYTHON_VERSION=3.5
  # Disable if not needed
  # - LABCONTROL_DEBUG_LEVEL=DEBUG
before_install:
  - sudo apt-get install libevent-dev
  - redis-server --port 7777 &
  - wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
  - chmod +x miniconda.sh
  - ./miniconda.sh -b
  - rm miniconda.sh
  - df -h
  - export PATH=/home/travis/miniconda3/bin:$PATH

  # Add conda-forge to the list of channels to search for packages
  # (May help with libgfortran not being found recently)
  - conda config --append channels conda-forge
  # Update conda itself
  - conda update --yes conda
  # node-qunit-puppeteer is a runner.js like interface for
  # headless-chrome and qunit.
  # node-qunit-puppeteer installs its own chromium as a dependency.
  # hence, a separate chrome installation is not required.
  #
  # also, install "prettier" for front-end code auto formatting.
  - npm install -g node-qunit-puppeteer prettier
install:
  # Hard limit for transaction log, to prevent VHD from filling during tests
  - psql -c "ALTER SYSTEM SET max_wal_size=2"
  - psql -c "ALTER SYSTEM SET wal_keep_segments=0"
  - psql -c "SELECT pg_reload_conf()"
  # Verify log directory exists, postgresql processes exist, and postgresql is
  # listening on port
  - sudo find /var/lib/postgresql | grep -i log
  - ps -A | grep post
  - netstat -tulpn
  # Create the Qiita environment
  - travis_retry conda create -q --yes -n qiita python=3.6 pip libgfortran numpy nginx
  - source activate qiita
  - pip install sphinx sphinx-bootstrap-theme coveralls
  - pip install https://github.com/biocore/qiita/archive/dev.zip --no-binary redbiom
  # as we don't need redbiom we are going to use the default redis port
  - sed 's/PORT = 7777/PORT = 6379/g' $HOME/miniconda3/envs/qiita/lib/python3.6/site-packages/qiita_core/support_files/config_test.cfg > config_test.cfg
  - export QIITA_CONFIG_FP=${PWD}/config_test.cfg
  # starting nginx
  - mkdir /home/travis/miniconda3/envs/qiita/var/run/nginx/
  - wget https://github.com/biocore/qiita/archive/dev.zip -O qiita-dev.zip
  - unzip qiita-dev.zip
  - nginx -c ${PWD}/qiita-dev/qiita_pet/nginx_example.conf
  - qiita-env make --no-load-ontologies
  - supervisord -c ${PWD}/qiita-dev/qiita_pet/supervisor_example.conf
  - sleep 10 # give enough time to the webserver to start
  - cat /tmp/supervisord.log
  - source deactivate
  - git clone https://github.com/nicolasff/webdis
  - pushd webdis
  - make
  - ./webdis &
  - popd
  # Deactivate the Qiita environment
  - conda deactivate
  # Set the labcontrol config file
  - sed "s#CERTIFICATE_FILEPATH=#CERTIFICATE_FILEPATH=$PWD/support_files/server.crt#g" labcontrol/db/support_files/skeleton_labcontrol.cfg > ~/.labcontrol.cfg.1
  - sed "s#KEY_FILEPATH=#KEY_FILEPATH=$PWD/support_files/server.key#g" ~/.labcontrol.cfg.1 > ~/.labcontrol.cfg
  # Install labcontrol
  - travis_retry conda create --yes -n labcontrol python=$PYTHON_VERSION pip nose flake8 mock
  - source activate labcontrol
  - python --version
  - travis_retry pip install -U pip
  # print nosetests version:
  # Note that this doesn't execute tests before LC has been installed.
  - nosetests -V
  - travis_retry pip install nose-exclude
  - travis_retry pip install sphinx sphinx-bootstrap-theme coveralls
  - travis_retry pip install https://github.com/qiita-spots/qiita_client/archive/master.zip
  - travis_retry pip install .
  - mkdir -p support_files
  - openssl req -x509 -nodes -days 365 -newkey rsa:2048 -keyout support_files/server.key -out support_files/server.crt -subj "/C=US/ST=CA/L=LaJolla/O=/CN=localhost"
  # Apply the labcontrol patches to the database
  - psql -d qiita_test -f labcontrol/db/support_files/db_patch.sql
  - psql -d qiita_test -f labcontrol/db/support_files/db_patch_manual.sql
  # Verify db population
  # TODO: extend to labman schema
  - psql -d qiita_test -c 'select * from qiita.study;'
  - labcontrol patch
script:
  - python labcontrol/gui/js_tests/js_tester.py all-tests
  - nosetests --exclude-dir=labcontrol/gui/js_tests --with-doctest --with-coverage -v --cover-package=labcontrol
  - flake8 labcontrol setup.py scripts/*
  # Run prettier to verify that the JS/CSS ("front end") code doesn't need any
  # stylistic adjustments.
  - make festylecheck
  - labcontrol/db/tests/tester.py integration_tests
  - labcontrol/db/tests/tester.py stress_tests --num_plates_amplicon 2 --num_plates_shotgun 2
  - labcontrol start-webserver &
  - LABCONTROL_PID=$!
  - sleep 10
  - kill $LABCONTROL_PID
addons:
  postgresql: "9.5"
services:
  - redis-server
  - postgresql
after_success:
  - coveralls