Bio bank

Introduction

This project provides an administrative interface for managing tissue sample collections and associated samples. It enables efficient tracking and organisation of valuable biological data for research and clinical purposes.

Key Features:

• Visualise Collections: View a comprehensive list of existing sample collections.
• Explore Samples: Deep dive into the details of samples associated with each collection.
• Expand Resources: Add new samples to existing collections.
• Catalog New Collections: Organize your biological data by creating new collections with ease.

Getting Started

Prerequisites:

To run Bio Bank locally, ensure you have the following tools installed

• Node.js(v16+)
• NPM
• MySQL

Installation:

1. clone repository:

git clone https://github.com/Kehindecodes/Bio_Bank

2. Navigate to project directory:

cd Bio_Bank

3. Install dependencies :

npm install

3. Install backend and frontend dependencies :

# Install backend dependencies
cd server
npm install

# Install frontend dependencies
cd client
cd bio-bank
npm install

4. Configure Database:

• Edit server/src/services/database.config.js with your MySQL credentials.

5. Run Application from root folder:

npm run dev

This command starts both the backend server and frontend client concurrently.

6. Access Application:

• Launch your web browser and navigate to the following address:

http://localhost:5173/

This will open the Bio Bank application in your browser, ready for use.

Project Structure

The project is organized into server and client folders, each with its own set of files and directories

Backend

Technology Used :

• Node.js
• Express.js
• Sequelize(ORM for MySQL)

Setup:

1. Navigate to server directly

cd server

2. Install Dependencies

npm install

3. Configure database in server/src/services/database.config.js
4. Run backend server

npm run dev

Environment Variables:

• DB_HOST: Your MySQL server hostname or IP address.
• DB_USER: Your MySQL username.
• DB_PASSWORD: Your MySQL password.
• DB_NAME: Your MySQL database name.

API Endpoints:

All API responses are delivered in JSON format, with clear error codes and messages for handling unsuccessful requests

• GET /api/v1/collections : Retrieve a list of collections
• POST /api/v1/collections : Create a new collection
• GET /api/v1/collections/:id/samples : Retrieve samples for a specific collection
• POST /api/v1/collections/:id/samples : Add a new sample to a specific collection

Testing:

The backend API endpoints are covered by a suite of automated tests to ensure their correctness and robustness. These tests use the supertest library to simulate HTTP requests and assert expected responses.

Run backend test :

npm test

Database Schema:

The MySQL database includes tables for collections and samples. Refer to server/src/models for the Sequelize model definitions.

Frontend

Technology used:

• React.js
• TailwindCSS

Setup:

1. Navigate to frontend directory

cd client
cd bio-bank

2. Install dependencies

npm install

3. Run frontend development server

npm run dev

Folder Structure:

The src folder contains the main React components, organized into directories such as components and pages and it also has an api folder too.

Component Details:

• CollectionTable: Dynamically displays a list of collections with sorting functionalities.
• Pagination: Enables users to easily navigate through pages of data when collections are numerous.
• FormModal: A reusable modal window used for both creating new collections and adding new samples.
• SampleTable: Presents a table of samples associated with a specific collection

State Management:

The state is managed using React's local component state and the useSWR library for data fetching.

Data Validation:

Frontend forms utilize react-hook-form library for validation to ensure accurate data entry before submitting requests.

Styling:

Tailwind CSS is used for styling, and the configuration can be found in tailwind.config.js.