Docker configuration for GRYC

The project contain 3 docker-compose files:

• docker-compose.yml (used in prod and dev)
• docker-compose.override.yml (used in dev)
• docker-compose.prod.yml (used in prod)

When you are in dev, you just use the command docker-compose build|create|up|start..., docker-compose automatically use: docker-compose.yml and docker-compose.override.yml. But in production, you need manually define the files with the option-f: docker-compose -f docker-compose.yml -f docker-compose.prod.yml build|create|up|start...

1. Before install

1.1. Configure Elasticsearch on Server

In this Docker configuration, we used Elasticsearch, but it need we set a variable in stsctl.conf, else it doesn't work.

The vm_map_max_count setting should be set permanently in /etc/sysctl.conf:

$ grep vm.max_map_count /etc/sysctl.conf
vm.max_map_count=262144

To apply the setting on a live system type: sysctl -w vm.max_map_count=262144

1.2. Available variables

In the .env file you find all variables that permit to configure the server environment, and the app.

1. NGINX_EXPOSED_PORT

   Define the nginx exposed port on the server, the port you need use to access to the app.

2. DATABASE_NAME, DATABASE_HOST, DATABASE_USER, DATABASE_PASSWORD, DATABASE_ROOT_PASSWORD

   Variables to configure the MySQL database. (You normally don't need edit DATABASE_HOST, if you do, check docker-compose.yml to adapt)

3. ELASTICSEARCH_HOST, ELASTICSEARCH_PORT

   Idem, for elasticsearch. (You normally don't need edit it, if you do, check docker-compose.yml to adapt)

4. RABBITMQ_HOST, RABBITMQ_PORT, RABBITMQ_USER, RABBITMQ_PASSWORD

   Idem for RabbitMQ.

5. SMTP_HOST, SMTP_PORT, SMTP_USER, SMTP_PASSWORD

   Configure the SMTP server, the application use a tls encryption to send mail.

6. MAILER_SENDER_ADDRESS

   The email, that appear at expeditor in emails.

7. MAILER_SENDER_NAME

   The name that appear as expeditor.

8. SYMFONY_SECRET, SYMFONY_ENV, SYMFONY_DEBUG

   Some symfony variables that define the environment and the debug. The SYMFONY_SECRET, must be cganged and can be generated with:

      openssl rand -hex 20
   

9. RECAPTCHA_PUBLIC_KEY, RECAPTCHA_PRIVATE_KEY

   This token are used to protect the forms in the app. You can have it on https://www.google.com/recaptcha, and get an Invisible reCAPTCHA

2. How to install the Prod version

1. Clone the repository in your www folder, or in an other.

    git clone https://github.com/mpiot/gryc-docker.git gryc
    cd gryc
   

   The next points assume that the files are in the folder called /var/www/gryc.

2. Copy .env files and fill them

    cp .env.dist .env
   

   Then, edit the .env file and fill them with your data. This file has a dual purpose:

   • define vars for contruct Docker containers (like the db passwrod)
   • define vars used in the application (like the db password too)

3. Build images, create containers, construct network and volumes, and start created containers

    docker-compose -f docker-compose.yml -f docker-compose.prod.yml up -d
   

4. Create and populate the Elasticsearch database (may be done manually after containers started)

    docker exec -it gryc-app bin/console fos:elastica:populate
   

5. Configure your reverse proxy (see 4)

6. Finished

   Your GRYC instance is ready to use!

3. How to install the dev version

The installation of the dev version is similar to the prod but we don't use the same docker-compose.yml files, and you need to download the source code of GRYC. We don't use volume to store it, to permit edit the code and permit change usage per Docker.

1. Clone the repository in your workdir folder, or in an other.

    cd ~
    git clone https://github.com/mpiot/gryc.git
    git clone https://github.com/mpiot/gryc-docker.git
    cd gryc-docker
   

   Here we clone the gryc and the gryc-docker repositories.

2. Copy .env files and fill them

    cp .env.dist .env
   

   Then, edit the .env file and fill them with your data. This file has a dual purpose:

   • define vars for contruct Docker containers (like the db passwrod)
   • define vars used in the application (like the db password too)

3. Build images, create containers, construct network and volumes, and start created containers

    docker-compose up -d
   

   When not files are given to docker-compose, it use docker-compose.yml and docker-compose.override.yml

   You can edit ports in docker-compose.override.yml

4. In Dev, the container doesn't automatically update the database, then you must do it manually

    docker exec -it gryc-app bin/console doctrine:migrations:migrate
   

5. Create and populate the Elasticsearch database (may be done manually after containers started)

    docker exec -it gryc-app bin/console fos:elastica:populate
   

6. In prod the docker image contains compiled assets, but not in git repo.

   5.1. Install node dependencies:

    docker run -v /path/to/gryc/folder:/var/www/html -w /var/www/html -i -t node:8 yarn install
   

   5.2. Compile assets:

    docker run -v /path/to/gryc/folder:/var/www/html -w /var/www/html -i -t node:8 yarn prod|dev|watch
   

   prod to compile with uglify filter

   dev to compile without uglify filter

   watch to automatically process a dev compilation each time a file is modified

7. Give access rights to the container for var/ and files/ folders

    setfacl -dR -m u:33:rwX -m u:YOUR_USERNAME:rwX var/ files/
    setfacl -R -m u:33:rwX -m u:YOUR_USERNAME:rwX var/ files/
   

8. Configure your reverse proxy (see 4)

9. Finished

   Your GRYC instance is ready to use!

4. How to configure Haproxy

To access the site on your hostname, you need to configure a reverse proxy, that transfert traffic on the container.

An example of configuration with haproxy is available in the folder reverse-proxy. Adapt the config, with the real domain name, and the port of the docker container, you also can remove parts about ssl.

You need to install at least the v1.8 of HaProxy to use http2. (eg: https://haproxy.debian.net/)

You can access to the HaProxy management page on: http://localhost:9000/haproxy_stats (you can change it in the conf)

4. How to save files (Blast, EMBL, ...)

docker run --rm --volumes-from gryc-app -v /folder/to/put/backup:/backup debian tar -zcf /backup/nom-fichier-backup.tar.gz -C /var/www/html/files .

5. How to dump and restore the database

To dump the database:

docker exec gryc-db /usr/bin/mysqldump -u root --password=ROOT_PASSWORD DATABASE_NAME > backup.sql

To restore the database:

cat backup.sql | docker exec -i gryc-db /usr/bin/mysql -u root --password=ROOT_PASSWORD DATABASE_NAME

6. How to install xDebug

1. Enter in the container

    docker exec -it gryc-app bash
   

2. Use the followed commands

    pecl install xdebug-2.5.0 && docker-php-ext-enable xdebug
   

3. Restart the container

    docker-compose restart
   

7. How to update prod version

docker-compose -f docker-compose.yml -f docker-compose.prod.yml stop
docker rm gryc-nginx gryc-app
docker volume ls
docker volume rm <APP_SRC VOLUME>
docker pull mapiot/gryc:latest 
docker-compose -f docker-compose.yml -f docker-compose.prod.yml up -d