adhikasp / phycus

Service used for curation of Haplotype Frequency

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 start the server using the IP address Docker has assigned. Use docker-machine ip to retrieve it. You'll use it to replace localhost in jdbc:mysql://localhost:3306/hfcusdb when you start your server. (See the command below.)

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 8 on Windows:

 java  -Dspring.datasource.url="jdbc:mysql://your-ip-address-here:3306/hfcusdb" -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.