New SUSHI 2025

Rails v8 API and FastAPI (backend) + Next.js (frontend) implementation of the SUSHI bioinformatics system.

1. Prerequisites

• Ruby 3.3.7
• Python 3.12.x
• Node.js 22.16.0
• Git

2. Environment Setup

(on fgcz-r-029)

1. Load Required Modules

bash module load Dev/Ruby/3.3.7 module load Dev/node/22.16.0

2. Clone Repository

bash cd /misc/fgcz01/sushi/ git clone git@github.com:fgcz/new_SUSHI_2025 cd new_sushi_2025

3. Backend Setup

```bash cd backend

Configure Bundler for local gem installation

bundle config set --local path 'vendor/bundle'

Install gems

bundle install ```

4. Frontend Setup

```bash cd ../frontend

Install dependencies

npm install ```

2. Development Environment Setup (Limited Compilation Environment)

1. Prepare Libraries on Compilation-Capable Machine: ```bash # Clone repository git clone git@github.com:fgcz/newSUSHI2025 cd newsushi2025

Load required modules

module load Dev/Ruby/3.3.7 module load Dev/node/22.16.0

Install backend dependencies

cd backend bundle config set --local path 'vendor/bundle' cp -r /misc/fgcz01/sushi/newSUSHI2025/backend/vendor .

Run tests to verify setup

bundle exec rspec

Install frontend dependencies

cd ../frontend cp -r /misc/fgcz01/sushi/newSUSHI2025/frontend/node_modules .

Run tests to verify setup

npm test ```

1. Database Setup (SQLite3, for development): ```bash cd ../backend/ # Setup database bundle exec rails db:create bundle exec rails db:migrate

Run API server

bundle exec rails s -b fgcz-h-037.fgcz-net.unizh.ch -p 4000 ```

1. Frontend Verification: ```bash cd frontend

Start development server

npm run dev -- --port 4001 ```

4. Production Deployment Setup

TODO: update

1. Prerequisites

• Full development environment with compilation tools
• All system libraries required for native gem compilation
• Proper SSL certificates and security configurations

2. Backend Production Setup

```bash cd backend

Configure Bundler for production

bundle config set --local path 'vendor/bundle'

Install production dependencies

bundle install

Database setup

RAILSENV=production bundle exec rails db:create RAILSENV=production bundle exec rails db:migrate

Precompile assets (if needed)

RAILS_ENV=production bundle exec rails assets:precompile

Run production server

RAILS_ENV=production bundle exec rails server -p 4000 ```

3. Frontend Production Setup

```bash cd frontend

Install production dependencies

npm ci --only=production

Build application

npm run build

Start production server

npm start ```

4. Docker Deployment

```bash

Build images

docker-compose build

Deploy

docker-compose up -d

Health check

docker-compose ps ```

5. Test

1. Backend Tests

bash cd backend bundle exec rspec # Run all tests bundle exec rspec --format doc # Verbose output

2. Frontend Tests

bash cd frontend npm test # Interactive mode npm run test:watch # Watch mode npm run test:coverage # With coverage npm run test:ci # CI mode

6. Project Structure

new_sushi_2025/ ├── backend/ # Rails v8 API │ ├── app/ │ ├── config/ │ ├── spec/ # RSpec tests │ └── vendor/bundle/ (ignored) ├── frontend/ # Next.js app │ ├── app/ │ ├── __tests__/ │ └── node_modules/ (ignored) └── README.md

7. Environment Variables

Create these files if needed (not committed to repository):

1. Backend

```bash

backend/.env

DATABASEURL=sqlite3:db/development.sqlite3 RAILSENV=development ```

2. Frontend

```bash

frontend/.env.local

NEXTPUBLICAPI_URL=http://localhost:4000 ```

8. Architecture

• Backend: Rails v8 API-only mode, FastAPI (later)
• Frontend: Next.js 15 with TypeScript
• Database: SQLite (development), PostgreSQL (production)
• Testing: RSpec (backend), Jest + React Testing Library (frontend)
• Styling: Tailwind CSS