Haplotype Frequency Curation

Service to help curate Haplotype Frequencies.

Development Overview

Pre-requisites:

• JDK 8
• Apache Maven
• Docker

Build the application

mvn clean package

Setup Database

The project is setup to use mysql Docker instance for local development.

cd db/
docker-compose up -d

The phpMyAdmin page should be available at http://localhost:9999/. For Windows, you will need to use the IP of the docker VM instead of localhost. You can retrieve the IP with docker-machine ip. Usually it's 192.168.99.100. Login with hfcus_user user and hfcus_user1 as password.

Use docker-compose stop and docker-compose rm to stop and remove the db containers.

Run the application

Special step on windows

On Windows, you need to change src/main/resources/application.properties and replace localhost with the IP of your docker machine, then recompile. Use docker-machine ip to retrieve it.

Starting the application

Start your server as a simple java application
Check your JDK version with java -version

With Java 8:

 java -jar target/service-haplotype-frequency-curation-0.0.1.jar

With Java 9:

java --add-modules java.xml.bind -jar target/service-haplotype-frequency-curation-0.0.1.jar

You can view the api documentation in swagger-ui by pointing to http://localhost:8080

Using the service

See client/ directory for examples on using it from various languages. Eg. for Perl

Read the User Guide

See docs/ directory for a user guide and examples of how the service is used in practice.