diff options
Diffstat (limited to '.github')
| -rw-r--r-- | .github/workflows/main.yml | 40 |
1 files changed, 22 insertions, 18 deletions
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 94b0db75..2fd9a886 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -13,32 +13,36 @@ jobs: runs-on: ubuntu-latest container: bonfacekilz/python2-genenetwork2:latest - services: - mariadb: - image: mariadb:latest - ports: - - 3306:3306 - env: - MYSQL_USER: gn2 - MYSQL_PASSWORD: mysql_password - MYSQL_ALLOW_EMPTY_PASSWORD: yes - MYSQL_DATABASE: db_webqtl_s - MYSQL_ROOT_PASSWORD: mysql_password - options: --health-cmd="mysqladmin ping" --health-interval=5s --health-timeout=2s --health-retries=3 - steps: + # First start with mariadb set then checkout. The checkout gives + # the mysqld enough time to start + - name: Set up mariadb + run: | + mysql_install_db --user=mysql --datadir=/usr/local/mysql + # Wait for the mysqld_safe process to start + mysqld_safe --user=mysql --datadir=/usr/local/mysql & + # Use v1 of checkout since v2 fails - name: Checkout Project uses: actions/checkout@v1 - # Redis is required by some of the tests + # Redis is required by some of the tests 6379 - name: Start Redis run: | - redis-server --daemonize yes + /gn2-profile/bin/screen -dmLS redisconn /gn2-profile/bin/redis-server + + # Redis is required by some of the tests 6379 + - name: Bootstrap tables + run: | + mysql -u root -e "SHOW DATABASES;" + mysql -u root -e "CREATE DATABASE db_webqtl_s;" + mysql -u root -e "CREATE USER 'gn2'@'localhost' IDENTIFIED BY 'mysql_password';" + mysql -u root -e "GRANT ALL PRIVILEGES ON *.* TO 'gn2'@'localhost';FLUSH PRIVILEGES;" - name: Run the unit tests run: | - mkdir -p /genotype_files/genotype/json - env GN2_PROFILE=/usr/gn2-profile TMPDIR=/tmp SERVER_PORT=5004 \ - GENENETWORK_FILES=/genotype_files/ bash bin/genenetwork2 \ + env GN2_PROFILE=/gn2-profile \ + TMPDIR=/tmp SERVER_PORT=5004 \ + WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \ + GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ etc/default_settings.py -c -m unittest discover -v |