Puppet module to deploy glowing bear backend

How to install

sudo apt-get update --fix-missing

# For Debian 9 and Ubuntu 18.04
sudo apt install puppet

sudo apt install postgresql

# For Ubuntu 16.04
wget https://apt.puppetlabs.com/puppet5-release-xenial.deb
sudo dpkg -i puppet5-release-xenial.deb
sudo apt update
sudo apt install puppet5-release

# Install puppet modules
sudo puppet module install puppet-archive -v 3.2.1
sudo puppet module install puppetlabs-java -v 3.3.0
sudo puppet module install puppetlabs-postgresql -v 5.11.0

# Check Puppet version, Puppet 4.8 and Puppet 5 should be fine.
puppet --version

Note: module will create a database and user with password (see parameters here) if it does note exist.

Install module

git submodule add https://github.com/thehyve/puppet-gb_backend.git gb_backend

Dependencies

The instructions are for installing

• the Keycloak identity provider,
• the TranSMART API server, and
• the Glowing Bear user interface for the backend.

Install the transmart_core and glowing_bear modules

Copy the transmart_core and glowing_bear module repositories to the /etc/puppetlabs/code/modules directory:

cd /etc/puppetlabs/code/modules
git clone https://github.com/thehyve/puppet-transmart_core.git transmart_core
git clone https://github.com/thehyve/puppet-glowing_bear.git glowing_bear

Parameters

Keycloak parameters

Keycloak parameters. They should match with that ones that frontend glowing bear application uses.

hiera key	default value	description
gb_backend::keycloak_server_url		keycloak url that used. e.g. https://keycloak.example.com/auth
gb_backend::keycloak_realm		keycloak realm.
gb_backend::keycloak_client_id		keycloak client id.
gb_backend::keycloak_offline_token		keycloak offline token.

Application parameters

Please note that transmart.api-version hardcoded to v2.

hiera key	default value	description
gb_backend::transmart_server_url		transmart url that used. e.g. https://transmart.example.com

Application db parameters

Database parameters used to create database if it does not exist and used by the application to establish connnection. Note: Creationg of the databse supported only for localhost db host. PostgeSQL is used by default at the moment.

Hiera key	Default value	Description
gb_backend::db_user	gb	Database user that used by the application to connect to the database.
gb_backend::db_password	gb	The user password to the database.
gb_backend::db_host	localhost	The database server host name.
gb_backend::db_port	5432	The database server port.
gb_backend::db_name	gb_backend	The database name.

Resource where to get the application

Hiera key	Default value	Description
gb_backend::nexus_url	https://repo.thehyve.nl	The Nexus/Maven repository server.
gb_backend::reporsitory	snapshots	The repository to use. releases or snapshots are only valid options.

OS parameters

Hiera key	Default value	Description
gb_backend::user	gb	System user that runs the application.
gb_backend::user_home	/home/${user}	The user home directory.

Misc. application parameters

Hiera key	Default value	Description
gb_backend::vesion	0.1-SNAPSHOT	The version of application to install.
gb_backend::app_port	8083	The port the application runs on.

Query subscription notification parameters

Hiera key	Default value	Description
gb_backend::notifications_enabled	false	Enable notification for query subscriptions.
gb_backend::notifications_sets	20	Number of sets.
gb_backend::notifications_trigger_hour	0	Hour for daily notification trigger.
gb_backend::notifications_trigger_minute	0	Minute for daily notification trigger.
gb_backend::notifications_client_app_name	Glowing Bear	Name of the client application on behalf of which gb-backend will send notification email
gb_backend::notifications_client_app_url		URL of the client application
gb_backend::sender_email		Email address used in "from" field in the emails sent by the glowing bear.

Manage systemd services

Start the gb-backend service:

sudo systemctl start gb-backend

Check the status of the service:

sudo systemctl status gb-backend

Stop the service:

sudo systemctl stop gb-backend

Check log of the service

sudo journalctl -u gb-backend.service

Development

Test

The module has been tested on Ubuntu 16.04 with Puppet version 5.5.0. There are some automated tests, run using rake.

A version of ruby before 2.3 is required. rvm can be used to install a specific version of ruby. Use rvm install 2.1 to use ruby version 2.1.

The tests are automatically run on our Bamboo server: PUPPET-PUPPETTS.

Rake tests

Install rake using the system-wide ruby:

yum install ruby-devel
gem install bundler
export PUPPET_VERSION=4.8.2
bundle

or using rvm:

rvm install 2.3
gem install bundler
export PUPPET_VERSION=4.8.2
bundle

Run the test suite:

rake test

License

Copyright © 2019 The Hyve.

The puppet module for gb-backend is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.