aboutsummaryrefslogtreecommitdiff
path: root/.github
diff options
context:
space:
mode:
authorBonfaceKilz2021-05-11 12:10:37 +0300
committerBonfaceKilz2021-05-11 13:24:54 +0300
commit75b378f757979af1d6fdaff3f3abde0599c5f744 (patch)
treeca5a92c3d37c7663c91c32535afee3141addecae /.github
parent4538c0ad693ae94ebda5f0bf39678d776c0c8297 (diff)
downloadgenenetwork2-75b378f757979af1d6fdaff3f3abde0599c5f744.tar.gz
workflows: main.yml: Use mariadb as a service
Diffstat (limited to '.github')
-rw-r--r--.github/workflows/main.yml30
1 files changed, 13 insertions, 17 deletions
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index b09f2f1d..a2925e08 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -12,16 +12,19 @@ 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
@@ -31,17 +34,10 @@ jobs:
run: |
/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: Start Genenetwork as a Background Task
run: |
- /gn2-profile/bin/screen -dmL bash -c "env GN2_PROFILE=/gn2-profile \
+ /gn2-profile/bin/screen -dmLS gn2conn
+ bash -c "env GN2_PROFILE=/gn2-profile \
TMPDIR=/tmp SERVER_PORT=5004 \
WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \
GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \