About Genolink

Genolink is a middleware solution enabling seamless integration and interoperability between genotype databases and Genesys-PGR (genebank passport repository). Genolink is funded as part of the Australian Grains Genebank Strategic Partnership, a $30M joint investment between the Victorian State Government and Grains Research and Development Corporation (GRDC) that aims to unlock the genetic potential of plant genetic resources for the benefit of the Australian grain growers. https://agriculture.vic.gov.au/crops-and-horticulture/the-australian-grains-genebank

Genolink Features

• Connects genotype databases and Genesys-PGR without the need for data duplication, reducing synchronization issues and overheads.

• Provides real-time access to passport and genotype data, ensuring users always have current information.

• Allows users to filter accessions based on passport information or specified lists before retrieving related genotype data.

• Supports integration with multiple genomic platforms, enabling comprehensive data retrieval and consolidation.

• Provides APIs for independent user-facing tools like the web-based genomic visualization tool Pretzel to leverage its functionality.

• Reduces data redundancy by avoiding the need for local duplicate copies of databases.

• Streamlines the process of managing large-scale genotype data from global wheat genebanks.

Setup Instructions

Note: For any placeholder values (e.g., <your_db_username>, <your_db_password>, etc.), please replace them with the correct data that you need to use.

Manual Setup

Prerequisites

Before you begin, ensure you have the following installed:

• Node.js (version 14 or higher)
• NPM (version 6 or higher)
• MySQL (server and client)

Setup Steps

1. Clone the Project

Clone the project repository to your local machine from GitHub:

git clone <repository_url>

2. Install Frontend Dependencies

Navigate to the 'front' directory and install dependencies:

npm install

3. Create .env File for Frontend

Create a .env file in the 'front' directory with the following content:

VITE_Genesys_OIDC_AUTHORITY=https://api.sandbox.genesys-pgr.org
VITE_Genesys_OIDC_CLIENT_ID=<ask Genesys support>
VITE_Genesys_OIDC_CLIENT_SECRET=<ask Genesys support>
VITE_Genesys_OIDC_REDIRECT_URI=http://127.0.0.1:3000
VITE_GENOLINK_SERVER=http://127.0.0.1:3000
VITE_GENESYS_SERVER=https://api.sandbox.genesys-pgr.org/api/v1/acn

4. Build Frontend

Build the frontend and move the generated 'dist' folder to the backend's root directory:

npm run build
mv dist ../back/

5. Install Backend Dependencies

Navigate to the back directory and install dependencies:

npm install

6. Install MySQL Client and Server

Install MySQL client and server:

sudo apt install mysql-server mysql-client

7. Create an Admin User

Open MySQL shell:

sudo mysql

Create a genolink user with the name "genouser":

CREATE USER '<your_db_username>'@'localhost' IDENTIFIED BY '<your_db_password>';

8. Create a Database

Create a database with the name corresponding to your_db_name:

CREATE DATABASE <your_db_name>;

9. Grant all previleges to the user

GRANT ALL PRIVILEGES ON <your_db_name>.* TO '<your_db_username>'@'localhost';
FLUSH PRIVILEGES;

10. Create .env File for Backend

Create a .env file in the 'back' directory with the following content:

DB_USERNAME=<your_db_username>
DB_PASSWORD=<your_db_password>
DB_NAME=<your_db_name>
DB_HOST=localhost
DB_DIALECT=mysql
GIGWA_SERVER=<your_gigwa_server_url>
GERMINATE_SERVER=<your_germinate_server_url>
GENOLINK_SERVER=http://127.0.0.1:3000
GENESYS_SERVER=https://api.sandbox.genesys-pgr.org/api/v1/acn
GENOLINK_SERVER_PORT=3000

11. Run the Application

Start the backend server by running the following in 'back' folder:

node index.js

12. Access the Application

Open your browser and navigate to http://localhost:3000 to use your application.

Docker Setup

Prerequisites

Before you begin, ensure you have the following installed:

• Docker (version 20 or higher)
• Docker Compose (version 1.29 or higher)

Option 1: Build Docker Image from Code

Setup Steps

1. Clone the Project

Clone the project repository to your local machine from GitHub:

git clone <repository_url>

2. Edit docker-compose.yml:

After cloning the project, open the docker-compose.yml file. This file contains placeholders (e.g., <your_db_username>, <your_db_password>, etc.) that need to be replaced with the correct values. Make sure to fill in these placeholders with the appropriate data.

3. Start Docker Containers

Navigate to the directory containing the docker-compose.yml file and run the following command to start the containers:

docker-compose up -d

4. Access the Application

Open your browser and navigate to http://127.0.0.1:3000 to use your application.

Option 2: Use Pre-built Docker Image from Docker Hub

Setup Steps

1. Create Docker Compose File

Create a docker-compose.yml file with the following content:

services:
  app:
    image: <genolink-dockerhub-repo>/genolink:latest
    ports:
      - '3000:3000'
    environment:
      # Frontend-Variables
      VITE_Genesys_OIDC_AUTHORITY: 'https://api.sandbox.genesys-pgr.org'
      VITE_Genesys_OIDC_CLIENT_ID: '<ask Genesys support for your OIDC Client ID>'
      VITE_Genesys_OIDC_CLIENT_SECRET: '<ask Genesys support for your OIDC Client Secret>'
      VITE_Genesys_OIDC_REDIRECT_URI: 'http://127.0.0.1:3000'
      VITE_GENOLINK_SERVER: 'http://127.0.0.1:3000'
      VITE_GENESYS_SERVER: 'https://api.sandbox.genesys.pgr.org'
      # Backend-Variables
      DB_USERNAME: '<your_db_username>'
      DB_PASSWORD: '<your_db_password>'
      DB_NAME: '<your_db_name>'
      DB_HOST: 'db'
      DB_DIALECT: 'mysql'
      GIGWA_SERVER: '<your_gigwa_server_url>'
      GERMINATE_SERVER: '<your_germinate_server_url>'
      GENOLINK_SERVER: 'http://127.0.0.1:3000'
      GENESYS_SERVER: 'https://api.sandbox.genesys.pgr.org/api/v1/acn'
      GENOLINK_SERVER_PORT: 3000
    depends_on:
      - db
    restart: always

  db:
    image: mysql:5.7
    environment:
      MYSQL_ROOT_PASSWORD: '<your_root_password>'
      MYSQL_DATABASE: '<same_as_your_db_name>'
      MYSQL_USER: '<same_as_your_db_username>'
      MYSQL_PASSWORD: '<same_as_your_db_password>'
    ports:
      - '3307:3306'

2. Start Docker Containers

Navigate to the directory containing the docker-compose.yml file and run the following command to start the containers:

docker-compose up -d

3. Access the Application

Open your browser and navigate to http://127.0.0.1:3000 to use your application.

Note: The Docker image will soon be available on Docker Hub.