api

PAN-GO API

A FastAPI application with GraphQL API powered by Strawberry GraphQL, Elasticsearch, and Poetry for dependency management.

Overview

This GraphQL API provides access to gene annotation data, supporting queries for:

• Gene annotations and statistics
• Evidence models
• Term models
• Autocomplete functionality

Prerequisites

• Python 3.10+
• Poetry (for dependency management)
• Docker & Docker Compose (for containerized deployment)
• Elasticsearch 8.5.0

Setup

1. Install Dependencies with Poetry

# Install Poetry if not already installed
curl -sSL https://install.python-poetry.org | python3 -

# Install project dependencies
poetry install

2. Environment Configuration

Copy the example environment file and configure your settings:

cp .env-example .env

Edit .env with your specific configuration (Elasticsearch host, ports, etc.)

Running the Application

Option 1: Local Development (without Docker)

Activate the Poetry virtual environment and run the server:

# Activate Poetry shell
poetry shell

# Run with Python
python main.py

# Or run with Poetry
poetry run python main.py

The API will be available at http://localhost:5000 (or your configured HOST_PORT)

Option 2: Docker Compose (Recommended for Production)

Choose the appropriate Docker Compose configuration based on your needs:

Standard 4G Configuration

docker-compose -f docker-compose-4G.yaml build
docker-compose -f docker-compose-4G.yaml up -d

4G Configuration with Kibana

docker-compose -f docker-compose-4G-kibana.yaml build
docker-compose -f docker-compose-4G-kibana.yaml up -d

2G Configuration (Lower Memory)

docker-compose -f docker-compose-2G.yaml build
docker-compose -f docker-compose-2G.yaml up -d

To stop the services:

docker-compose -f <docker-compose-file> down

API Access

GraphQL Playground

Once the server is running, access the GraphQL playground:

• Local: http://localhost:5000/graphql
• Docker: http://localhost:<HOST_PORT>/graphql

Development

Running Tests

# Run all tests
poetry run pytest

# Run with coverage
poetry run pytest --cov=src

# Run specific test file
poetry run pytest tests/test_graphql_api.py

Adding Dependencies

# Add a production dependency
poetry add package-name

# Add a development dependency
poetry add --group dev package-name

Code Quality

The project uses:

• Pydantic for data validation
• Strawberry GraphQL for GraphQL schema and resolvers
• Pytest for testing

Configuration Files

• log.ini - Logging configuration for general use
• log.local.ini - Logging configuration for local development
• log.docker.ini - Logging configuration for Docker containers
• pytest.ini - Pytest configuration
• pyproject.toml - Poetry dependencies and project metadata

Contact

For questions or issues, contact: pantherfeedback@yahoo.com