From c4ec08c1b544c05cce1c1247b8bc1afb741643e4 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 11 May 2021 13:38:47 +0300
Subject: workflows: main.yml: Remove mysql service and update gn2 b/g task

---
 .github/workflows/main.yml | 31 +++++++++++++++++--------------
 1 file 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
-
-- 
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