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| author | BonfaceKilz | 2021-05-11 13:38:47 +0300 |
|---|---|---|
| committer | BonfaceKilz | 2021-05-11 15:15:54 +0300 |
| commit | c4ec08c1b544c05cce1c1247b8bc1afb741643e4 (patch) | |
| tree | 2dcfd1eb153ddcce32d291791817ec4fb20a7492 /.github/workflows/main.yml | |
| parent | 75b378f757979af1d6fdaff3f3abde0599c5f744 (diff) | |
| download | genenetwork2-c4ec08c1b544c05cce1c1247b8bc1afb741643e4.tar.gz | |
workflows: main.yml: Remove mysql service and update gn2 b/g task
Diffstat (limited to '.github/workflows/main.yml')
| -rw-r--r-- | .github/workflows/main.yml | 31 |
1 files changed, 17 insertions, 14 deletions
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index a2925e08..c6b56a81 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -12,19 +12,16 @@ jobs: unittest: runs-on: ubuntu-latest container: bonfacekilz/python3-genenetwork2:00ba1f8 - services: - mysql: - image: mariadb:15.1 - env: - MYSQL_ALLOW_EMPTY_PASSWORD: yes - MYSQL_USER: gn2 - MYSQL_PASSWORD: mysql_password - MYSQL_DATABASE: db_webqtl_s - ports: - - 3306:3306 - options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --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 @@ -34,10 +31,17 @@ jobs: run: | /gn2-profile/bin/screen -dmLS redisconn /gn2-profile/bin/redis-server + # Initialise the tables + - 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: Start Genenetwork as a Background Task run: | - /gn2-profile/bin/screen -dmLS gn2conn - bash -c "env GN2_PROFILE=/gn2-profile \ + /gn2-profile/bin/screen -dm bash -c "env GN2_PROFILE=/gn2-profile \ TMPDIR=/tmp SERVER_PORT=5004 \ WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \ GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ @@ -59,4 +63,3 @@ jobs: GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ etc/default_settings.py -c \ $PWD/test/requests/links_scraper/genelinks.py - |