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Development Guide

Environment Setup

Using Conda (Recommended)

# Create environment with all dependencies
conda env create -f conf/conda.yaml
conda activate biobtree

### Build

```bash
# Using Makefile
make build

## Development vs Production

| Use Case | Tool | Purpose |
|----------|------|---------|
| **Production** | `bb.sh` | Full data processing with logging, versioning |
| **Development** | `biobtree` | Testing, debugging, limited data builds |

### Development Commands (biobtree)

```bash
# Build test database (limited entries per dataset)
./biobtree -d "uniprot,ensembl" test

# Update specific datasets (development)
./biobtree -d "uniprot" update

# Generate database
./biobtree generate

# Start web server
./biobtree web

# Query (server must be running)
curl "localhost:9292/ws/map/?i=BRCA1&m=>>ensembl&mode=lite"

Run Tests

# Single dataset
python3 tests/run_tests.py uniprot

# All datasets
python3 tests/run_tests.py all

Project Structure

biobtreev2/
├── src/                      # Go backend source
│   ├── biobtree.go           # Main CLI
│   ├── update/               # Dataset parsers
│   ├── generate/             # Database generation
│   ├── service/              # Web service
│   ├── query/                # Query parser
│   └── pbuf/                 # Protocol buffers
├── mcp_srv/                  # Python MCP server
├── conf/                     # Configuration files
├── tests/                    # Integration tests
└── docs/                     # Documentation

Adding a New Dataset

  1. Create parser: src/update/<dataset>.go
  2. Add config: conf/source.dataset.json
  3. Create tests: tests/datasets/<dataset>/
  4. Add docs: docs/datasets/<dataset>.md

See Adding Datasets for detailed guide.

Testing Philosophy

  • Integration tests over unit tests
  • Real database builds with limited data
  • Real web server queries
  • Reference data from official APIs

See Testing Guide for details.

Code Style

  • Go: Standard gofmt
  • Python: Black formatter
  • Comments only where logic isn't self-evident

Contributing

  1. Fork the repository
  2. Create a feature branch
  3. Make changes with tests
  4. Submit pull request

See Also