Docker instructions

To build the containers

./build.sh

To start a CBRAIN portal

cd Docker
source .env
USERID=`id -u` GROUPID=`id -g` docker-compose up

You can change the ports in .env if you wish.

Be careful to write down the CBRAIN admin password the first time you run docker-compose up.

The CBRAIN portal is then available at http://localhost:3000. It has a data provider, a bourreau, and the Diagnostics tool configured.

Files and directories

• Dockerfiles: Dockerfiles for the base CBRAIN, portal and bourreau images.
• entry_points: Bash scripts used as container entry points.
• init_portal: Ruby scripts used to initialize the database with a data provider, a bourreau and a tool.
• templates: Templates for portal and bourreau configuration files, instantiated in the entry point scripts.
• volumes: Directory where the mounted persistent volumes are created.

Startup process

The following containers are started (see configuration in docker-compose.yml):

1. MariaDB database
2. CBRAIN portal
3. CBRAIN bourreau
4. CBRAIN data provider

These containers mount volumes that are all located in volumes.

The entry point of the portal and bourreau are the bootstrap scripts ({portal,bourreau,data_provier}_bootstrap.sh). These scripts are run as user root to adjust the owners and permissions of the mounted volumes. They launch {portal,bourreau,data_provider}.sh as user cbrain.

Portal

The first time the portal starts, it:

• Loads the database schema
• Seeds the database
• Sanity checks the database
• Runs all the scripts in init_portal in the Rails console of the portal:
  • create_dp.rb: creates a local data provider, that persists files in volumes/data_provider.
  • create_bourreau.rb: adds a bourreau to the database, that corresponds to the bourreau container.
  • create_diagnostics_tool_config.rb: loads the Tools and creates a ToolConfig for Diagnostics on the previously-created bourreau.

Every time the portal starts, it:

• Waits for the database to be available.
• Installs the plugins in volumes/portal/plugins.
• Launches the BrainPortal application.

Bourreau

Every time the bourreau starts, it:

• Installs the plugins in volumes/bourreau/plugins.
• Waits for the portal to be started.
• Copy the portal's public key in its authorized_keys file.
• Starts sshd.

Data provider

Every time the data provider starts, it:

• Waits for the portal to be started.
• Copy the portal's public key in its authorized_keys file.
• Starts sshd.

Acknowledgements

This work has been funded in part by the European Union Seventh Framework Program (FP7/2007­2013) under grant agreement no. 604102 (HBP)

This work is part of SP8 of the Human Brain Project (SGA1).