Installation

This section describes the essential steps to deploy an RDP registry.

Requirements

Java 8+
MySQL 5.7+ or equivalent
SMTP mail server

Obtain a distribution of RDP

Download the JAR distribution from GitHub.

wget https://github.com/PavlidisLab/rgr/releases/download/v1.4.11/rdp-1.4.11.jar

The jar contains the core application, including an embedded webserver (Tomcat 8.5.x), a task scheduler, an in-memory cache, and much more!

Set up the MySQL database

Create the database and an associated user that the application will use to store and retrieve data.

create database '<database name>' character set utf8mb4;
create user  '<database username>'@'%' identified by '<database password>';
grant all on rdp.* to '<database username>'@'%';

If you're using MySQL 5.6 or prior, use the utf8 character set. It is a 3 bytes subset of the typical 4-bytes UTF-8 character encoding. Otherwise, you will face issues with the index size limit of 767 bytes due to some of our indexed columns containing 255 characters (4 * 255 = 1020 > 767, but 3 * 255 = 765).

Setup application.properties

In the working directory of the Web application, create an application.properties file that contains at least the following entries:

spring.profiles.active=prod

spring.datasource.url=jdbc:mysql://<database host>/<database name>
spring.datasource.driver-class-name=com.mysql.cj.jdbc.Driver
spring.datasource.username=<database username>
spring.datasource.password=<database password>

spring.mail.host=<mail host>
spring.mail.port=587
spring.mail.username=<mail username>
spring.mail.password=<mail password>
spring.mail.properties.mail.smtp.auth=true
spring.mail.properties.mail.smtp.starttls.enable=true

# Adjust this to your own network name
rdp.site.fullname=Rare Disease Model & Mechanism Network
rdp.site.shortname=RDMM

# This is very important for generating URLs
rdp.host=https://register.example.com
rdp.context=
rdp.mainsite=https://example.com/

rdp.site.contact-email=registry-help@example.com
rdp.site.admin-email=registry-admin@example.com

This file contains the database and SMTP credentials and various runtime configurations. Make sure it's only readable by the user that will run the instance.

Documentation for options with their default values are available in application.properties .

That should be enough to get the Web service started. Now you can launch it by issuing the following command:

java -jar rdp-1.4.11.jar

If your email server is not properly configured, you will see an error from the Spring Actuator health check. You can detect further issues by looking at the /admin/health endpoint with administrative privilege.

Create an administrative account

Use the registration page to create a user account and promote it to administrator privileges. Consider this to be a sanity check for your database and email server setup.

Once created, obtain its user identifier:

select user_id from user where email = '<your user email>';

Then add the ROLE_ADMIN (role_id is 1) role to that user:

insert into user_role (user_id, role_id) values ('<user_id>', 1);

Next, we will see how the Web application can be customized further.