From f184e2b4762d1ec5608d600dcb87406679212e39 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 22 Sep 2020 04:27:43 +0300
Subject: Add unittesting github action

* .github/workflows/main.yml: Add it.
---
 .github/workflows/main.yml | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 .github/workflows/main.yml

(limited to '.github/workflows/main.yml')

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
new file mode 100644
index 00000000..4c8db1c4
--- /dev/null
+++ b/.github/workflows/main.yml
@@ -0,0 +1,31 @@
+name: tests
+
+# Run actions when pushing to the testing branch or when you create a
+# PR against it
+on:
+  push:
+    branches: [ testing ]
+  pull_request:
+    branches: [ testing ]
+
+jobs:
+  unittest:
+    runs-on: ubuntu-latest
+    container: bonfacekilz/python2-genenetwork2:latest
+
+    steps:
+    # Use v1 of checkout since v2 fails
+    - name: Checkout Project
+      uses: actions/checkout@v1
+
+    # Redis is required by some of the tests
+    - name: Start Redis
+      run: |
+        redis-server --daemonize yes
+
+    - 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 \
+        etc/default_settings.py -c -m unittest discover -v
-- 
cgit v1.2.3


From 855558084a538ebdfec0bd43f829ba8d0d314a21 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 23 Sep 2020 03:05:42 +0300
Subject: Update github action to include mariadb service

* .github/workflows/main.yml: Add mariadb service. This makes the
build pass because somewhere(because of cyclic imports), a connection
to mariadb is required.
---
 .github/workflows/main.yml | 13 +++++++++++++
 1 file changed, 13 insertions(+)

(limited to '.github/workflows/main.yml')

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 4c8db1c4..94b0db75 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -13,6 +13,19 @@ 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:
     # Use v1 of checkout since v2 fails
     - name: Checkout Project
-- 
cgit v1.2.3


From 1907457a00f0f7a9f7e74d8955265c8635f03bce Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Fri, 25 Sep 2020 03:55:33 +0300
Subject: Update github action

* .github/workflows/main.yml: Set up a mariadb and redis within the GH
action.
(services): Remove mariadb service.
---
 .github/workflows/main.yml | 40 ++++++++++++++++++++++------------------
 1 file changed, 22 insertions(+), 18 deletions(-)

(limited to '.github/workflows/main.yml')

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
-- 
cgit v1.2.3