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CLAUDE.md

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

Project Overview

Shock is a RESTful, high-performance object storage platform for scientific data. It provides file storage with MongoDB-backed metadata, multi-cloud integration (S3, Azure, GCS, IBM TSM), and in-storage operations for bioinformatics data processing.

Build Commands

# Build the server (sets version from git tags)
./compile-server.sh

# Or directly with Go
CGO_ENABLED=0 go install -installsuffix cgo -v -ldflags="-X github.com/MG-RAST/Shock/shock-server/conf.VERSION=$(git describe --tags --long)" ./shock-server/

# Docker build
docker build -t mgrast/shock .

Running

shock-server -conf <path_to_config_file>

Testing

Tests run in Docker with MongoDB:

# Run all tests
./run-tests.sh all

# Run tests for a specific package
./run-tests.sh package ./shock-server/node

# Generate coverage report
./run-tests.sh coverage

# Clean test environment
./run-tests.sh clean

Test utilities are available in shock-server/test/ with mock implementations for database and filesystem.

Architecture

Entry Point

  • shock-server/main.go - Server initialization and HTTP routing via chi

Core Packages

Package Purpose
node/ Core data model - node CRUD, file management, indexing, ACLs, locations
file/ File handling and format-specific processors (FASTA, SAM, etc.)
auth/ Authentication mechanisms (basic, globus, oauth)
controller/node/ REST API endpoint handlers
conf/ Configuration management (INI + YAML files)
db/ MongoDB connectivity
location/ Storage location management for multi-cloud
user/ User management

Data Flow

REST API → Controllers → Node Package → MongoDB (metadata) + Filesystem/Cloud (data)

Configuration Files

  • Main config: INI format (e.g., shock-server.conf)
  • Storage locations: Locations.yaml
  • Node types: Types.yaml

Key API Routes

  • POST/GET/PUT/DELETE /node/{nid} - Node operations
  • /node/{nid}/acl/ - Access control
  • /node/{nid}/index/{type} - File indexing
  • /node/{nid}/locations/ - Storage locations
  • /preauth/{id} - Pre-authenticated access

Dependencies

  • Go 1.22
  • MongoDB - Required for metadata storage
  • gopkg.in/mgo.v2 - MongoDB driver
  • github.com/stretchr/testify - Testing assertions
  • AWS, Azure, and GCS SDKs for cloud storage

Profiling

Built-in pprof available on port 6060 when running.