🧬 Genomic API — Golang Microservice

A secure, containerized REST API for genomic data, built with Go, Gin, and PostgreSQL.

Features

• RESTful CRUD endpoints for genomes, samples, sequence files, variant files, and users
• JWT authentication
• PostgreSQL integration
• Docker & Docker Compose support
• Automatic DB schema and sample data initialization
• Live code reload in development (via Docker volume mount)
• Swagger UI documentation (/swagger/index.html)

Getting Started

Prerequisites

• Docker & Docker Compose
• (Optional) Go for local development

Setup

1. Copy .env.example to .env and update credentials, or create a .env file in the project root.
2. Build and run with Docker Compose:

   docker compose --env-file .env up --build

3. The API will be available at http://localhost:8080
4. Swagger UI available at http://localhost:8080/swagger/index.html

API Usage

• POST /api/login — obtain JWT token

• GET /api/genomes — list genomes

• POST /api/genomes — create genome

• GET /api/genomes/:id — get genome by ID

• PUT /api/genomes/:id — update genome

• DELETE /api/genomes/:id — delete genome

• GET /api/samples — list samples

• POST /api/samples — create sample

• GET /api/samples/:id — get sample by ID

• PUT /api/samples/:id — update sample

• DELETE /api/samples/:id — delete sample

• GET /api/sequence — list sequence files

• POST /api/sequence — create sequence file

• GET /api/sequence/:id — get sequence file by ID

• PUT /api/sequence/:id — update sequence file

• DELETE /api/sequence/:id — delete sequence file

• GET /api/variants — list variant files

• POST /api/variants — create variant file

• GET /api/samples/:id/variants — get variants for a sample

• DELETE /api/variants/:id — delete variant file

• GET /api/users — list users

• POST /api/users — create user

• GET /api/users/:id — get user by ID

• PUT /api/users/:id — update user

• DELETE /api/users/:id — delete user

Database

• Schema and sample data are initialized from genomic_schema.dmbl.sql on first run.
• To reset the DB, run:

  docker compose down -v
  docker compose --env-file .env up --build

Development

• Code changes are reflected live in the running container (no rebuild needed).
• Run locally with:

  go run main.go

• To update Swagger docs after changing handler annotations:

  swag init

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See INSTRUCTIONS.md for more details and commands.