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CLAUDE.md

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CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Application Overview

This is a FastAPI-based web API for the PRIDE Crosslinking Section, providing REST endpoints for managing and accessing crosslinking proteomics data. The API serves scientific data to external consumers and visualization tools.

Common Development Commands

Environment Setup

# Install dependencies using pipenv
pipenv install

# Activate virtual environment
pipenv shell

# Install development dependencies
pipenv install --dev

Running the Application

# Start the development server
python main.py

# The server will start on the port specified in database.ini (default: 8080)
# Access API docs at: http://localhost:{port}/pride/ws/archive/crosslinking/v3/docs

Testing

# Run tests using pytest
pytest

Architecture and Structure

Core Components

  • FastAPI Application: Main app defined in app/api.py with middleware for CORS, GZip compression, and request timing
  • Database Layer: PostgreSQL with SQLAlchemy ORM, Redis caching for performance
  • Route Organization: Modular router structure in app/routes/
    • pride.py: Core PRIDE functionality
    • pdbdev.py: PDB-Dev/IHM protein structure endpoints
    • xiview.py: Visualization data endpoints
    • parse.py: Data parsing and processing
    • shared.py: Common utilities

Configuration Management

  • Database Config: Environment variables with INI file fallbacks via db_config_parser.py
  • Logging: Configured through logging.ini
  • Settings: Key configuration in database.ini (auto-generated from default.database.ini)

Key Data Models

External models imported from separate package covering:

  • Project metadata (ProjectDetail, ProjectSubDetail)
  • Mass spectrometry data (Spectrum, SpectraData)
  • Peptide information (ModifiedPeptide, PeptideEvidence)
  • Database sequences and analysis results

API Versioning

  • Base URL: /pride/ws/archive/crosslinking/v3/
  • Version controlled through API_VERSION environment variable
  • OpenAPI documentation auto-generated

Deployment Pipeline

Local Development

  • Uses Pipenv for dependency management (Python 3.10)
  • Configuration through environment variables or INI files
  • Redis required for caching functionality

Production Deployment

  • Containerization: Docker multi-stage build (.Dockerfile -> Dockerfile)
  • Orchestration: Kubernetes on EBI Embassy Cloud OpenStack
  • Registry: GitHub Container Registry (GHCR)
  • CI/CD: GitHub Actions triggers on pride branch pushes
  • Environment: ConfigMaps for database and logging configuration

Branch Strategy

  • main: Main development branch
  • pride: Production deployment branch (triggers CI/CD)
  • dev: Current working branch

Database Integration

Connection Management

  • PostgreSQL primary database ("xiview")
  • Redis for caching with hiredis for performance
  • Session management through index.py
  • Async support via asyncpg

Data Processing

  • Scientific data handling with numpy, pandas, pyteomics
  • Mass spectrometry file parsing (pymzml, mzidentml-reader)
  • Crosslinking data visualization support

Security and Performance

  • API key authentication via python-jose
  • ORJSON for optimized JSON responses
  • GZip compression for responses >1KB
  • Request timing middleware with comprehensive logging
  • CORS configured for cross-origin requests