Update github action

* .github/workflows/main.yml: Set up a mariadb and redis within the GH
action.
(services): Remove mariadb service.

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