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 of accessions ot specified lists of genotype ids 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.

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 (Without Docker)

Prerequisites

Make sure you have installed:

• Node.js (v20+)
• npm (v6+)
• MySQL (server & 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_CLIENT_ID=<your_client_id>
VITE_Genesys_OIDC_CLIENT_SECRET=<your_client_secret>
VITE_GENOLINK_SERVER=<your_Genolink_server_address>   # e.g. https://genolink.plantinformatics.io OR http://127.0.0.1:3000
VITE_GENESYS_SERVER=https://api.sandbox.genesys-pgr.org

Genesys environment alignment

• If you are using Genesys sandbox, set:
  • VITE_GENESYS_SERVER=https://api.sandbox.genesys-pgr.org
  • Use the sandbox Client ID and Secret.
• If you are using Genesys production, set:
  • VITE_GENESYS_SERVER=https://api.genesys-pgr.org
  • Use the production Client ID and Secret.

Note: To obtain the correct Genesys OIDC Client ID and Secret for your Genolink server address (e.g. your domain or local 127.0.0.1:3000), please contact the Genesys support team. Sandbox and production have different Client IDs and Secrets. Make sure the URL and credentials belong to the same Genesys environment.

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 and configure MySQL:

_Install MySQL server and client for your OS _Start MySQL server _Create a database user and database:

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

7. 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>
GENOLINK_SERVER=<your_Genolink_server_address>   # e.g. https://genolink.plantinformatics.io OR http://127.0.0.1:3000
GENESYS_SERVER=https://api.sandbox.genesys-pgr.org
APP_PORT=<PORT> # e.g. 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 (Recommended)

Prerequisites

Make sure you have installed:

• Docker (v20+)
• Docker Compose (v1.29+)

Setup Steps

1. Clone the Project

Clone the project repository to your local machine from GitHub:

git clone <repository_url>

2. Create a .env file in the project root:

Example .env content:

DB_ROOT_PASSWORD=<your_root_mysql_password>
DB_USERNAME=<your_db_username>
DB_PASSWORD=<your_db_password>
DB_NAME=<your_db_name>
DB_HOST=db
DB_DIALECT=mysql
GENOLINK_SERVER=<your_Genolink_server_address>   # e.g. https://genolink.plantinformatics.io OR http://127.0.0.1:3000
GENESYS_SERVER=https://api.sandbox.genesys-pgr.org
APP_PORT=<PORT> # e.g. 3000
DB_PORT=<PORT> # e.g. 3306
VITE_Genesys_OIDC_CLIENT_ID=<your_Genesys_client_id>
VITE_Genesys_OIDC_CLIENT_SECRET=<your_Genesys_client_secret>
VITE_GENOLINK_SERVER=<your_Genolink_server_address>   # e.g. https://genolink.plantinformatics.io OR http://127.0.0.1:3000
VITE_GENESYS_SERVER=https://api.sandbox.genesys-pgr.org
VITE_PLATFORM=Gigwa
VITE_REQUIRE_GIGWA_CREDENTIALS=true
BASE_PATH=<optional_base_path> # e.g. /test OR leave empty for root

Genesys environment alignment

• If you are using Genesys sandbox, set:
  • VITE_GENESYS_SERVER=https://api.sandbox.genesys-pgr.org
  • Use the sandbox Client ID and Secret.
• If you are using Genesys production, set:
  • VITE_GENESYS_SERVER=https://api.genesys-pgr.org
  • Use the production Client ID and Secret.

Note: To obtain the correct Genesys OIDC Client ID and Secret for your Genolink server address (e.g. your domain or local 127.0.0.1:3000), please contact the Genesys support team. Sandbox and production have different Client IDs and Secrets. Make sure the URL and credentials belong to the same Genesys environment.

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 your_genolink_domain to use your application.