CCC-members / Docker-Loris_Deploy

Loris Docker deployment instructions:

• Requirements

  • Docker
  • Docker Compose

• Steps

  • Create base Docker image with Apache, PHP and Loris project using Dockerfile in php-apache directory
    • Notice that a custom install script is used in order to properly configure debian, which is unsupported by original install.sh
    • From within php-apache directory run
      • docker build -t loris-php .
  • Since the install.sh script must be run in interactive mode, you must execute
    • docker run -it --name loris-app loris-php bash
    • From within the container
      • Switch to lorisadmin user
        • sudo -s -u lorisadmin
      • Execute install script
        • cd tools
        • ./install.sh
        • Provide necessary script information, like project name (loris), and allow script to configure Apache
      • Restart apache server
        • sudo service apache2 restart
      • Exit the lorisadmin user and container - 2 x Ctrl+D
    • Create a new image with the changes made by the install script
      • docker commit loris-app loris-app
  • Run docker-compose.yml from loris-app directory in order to spin up application and database docker images
    • Create base directory for volume storage, as well as sub-directories for each of the volumes, e.g:
      • mkdir /data/loris-volumes
        • mkdir /data/loris-volumes/loris-app
        • mkdir /data/loris-volumes/loris-data
        • mkdir /data/loris-volumes/incoming-data
        • mkdir /data/loris-volumes/mysql-data
    • From within loris-app directory
      • Create a .env file which should contain the MySQL root password for database connection and the basepath for app volumes, e.g
        • MYSQL_ROOT_PASSWORD=loris-password
        • VOLUME_PATH=/data/loris-volumes
      • Spin up the app
        • docker-compose up or docker-compose up -d if you would like to run in background
  • Refer to the documentation online on how to configure application and database username/password. The application is accessible from the IP of the machine where it is running, port 80, or http://localhost if you are running it locally. The MySQL database is accessible at host db and the username/password for the database are root and whichever password you specified in .env file respectively

Steps to install Imaging Database

After configuring Loris by following all of the steps above, you may want to install the Imaging Database. In order to do that, you need to follow these steps:

• Stop and remove running loris app container and database
  • From within loris-app directory run
    • docker-compose down
• Build new loris-app image using Dockerfile in imaging directory
  • From within imaging directory run
    • docker build -t loris-app .
• Since the imaging_install.sh script must be run in interactive mode, you must first spin up the application and database with appropiate links - From within loris-app directory - docker-compose up -d - Enter the container - docker-compose exec loris bash - Grant lorisadmin ownership over /data directory - sudo chown -R lorisadmin:www-data /data - Execute install script - sudo -s -u lorisadmin - sudo apt-get update - ./imaging_install.sh - Provide necessary script information, like project name (loris) and database connection info from Loris deployment configuration. Database should be accessible at host db - Load minc environment - source /home/lorisadmin/.bashrc - Exit the lorisadmin user and container - 2 x Ctrl+D - Create a new image with the changes made by the install script - docker commit [loris container name] loris-app - Stop app - docker-compose down - Start again with new image - docker-compose up -d

Steps to install Data Query Tool

Stop running loris app - From within loris-app directory run - docker-compose down Spin up a new loris app using the docker-compose.yml file located in the data_query_tool directory - Create, inside the data_query_tool directory, a a .couchdb_env file which should contain the username and password for the couchbase db connection e.g - COUCHDB_USER=root - COUCHDB_PASSWORD=loris-password - Save the docker-compose.yml file inside the loris-app directory - From within loris-app directory run - mv docker-compose.yml docker-compose.yml.backup - Copy the docker-compose file from data_query_tool directory to the loris-app directory - From within loris-app directory run - cp ../data_query_tool/docker-compose.yml . - Create directories to store couchdb volumes, as subdirectories within the same $VOLUME_PATH as you specified in previous .env file, named couchdb-data and couchdb-conf, e.g: - mkdir /data/loris-volumes/couchdb-data
- mkdir /data/loris-volumes/couchdb-conf
- Spin up the app: - docker-compose up -d Set up CouchDB database by replicating existing database and running import scripts following instructions given in https://github.com/aces/Data-Query-Tool - Run a container mounting the loris-app volume in order to edit config.xml file to add the new CouchDB configuration parameters - docker run -it --rm -v loris-app_loris-app:/app alpine sh - vi /app/project/config.xml - Change the section <CouchDB>...</CouchDB> accordingly. Database host is couchdb and the port is 5984. Username and passwords are whatever you set in your .couchdb_env file. Database name is whatever you want (dqg is recommended), but please remember the name for subsequent steps - Exit the container Ctrl+D - Enter the loris-app container. From within loris-app directory run - docker-compose exec loris bash - Install erica and its dependencies in order to replicate existing database - sudo apt-get install -yy rebar erlang-src erlang-xmerl erlang-parsetools - wget https://people.apache.org/~dch/dist/tools/erica - mv erica /usr/bin - chmod +x /usr/bin/erica - Exit the container, commit changes and restart application - Ctrl-D - docker commit [loris container name] loris-app - docker-compose down - docker-compose up -d - Clone data query tools repo and replicate database, using configuration parameters you set in previous step - docker-compose exec loris bash - git clone https://github.com/aces/Data-Query-Tool.git - cd Data-Query-Tool - erica push http://$YOURCOUCHDBADMIN:$YOURCOUCHADMINPASS@$YOURSERVERNAME:5984/$YOURDATABASENAME - At this point, erica will output a message saying you can access db at a given URL. This is not possible unless you bind the port in the docker-compose file - In your Loris tools directory run the CouchDB_Import_* scripts - From /var/www/loris/tools directory run - php CouchDB_Import_Demographics.php - php CouchDB_Import_Instruments.php - php CouchDB_Import_MRI.php - Exit the container and test Loris deployment - Ctrl-D