Merge github.com:genenetwork/genenetwork2 into acenteno

1 files changed, 65 insertions, 0 deletions

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
new file mode 100644
index 00000000..8e2c7966
--- /dev/null
+++ b/.github/workflows/main.yml
@@ -0,0 +1,65 @@
+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/genenetwork2:latest
+
+    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 6379
+    - name: Start Redis
+      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 -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 \
+        etc/default_settings.py"
+
+    - name: Run the unit tests
+      run: |
+        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
+
+    # - name: Test for Broken Links
+    #   run: |
+    #     env GN2_PROFILE=/gn2-profile \
+    #     TMPDIR=/tmp\
+    #     WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \
+    #     GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \
+    #     etc/default_settings.py -c \
+    #     $PWD/test/requests/links_scraper/genelinks.py