LinkML Toolkit (lmtk)

A simple toolkit for working with LinkML schemas. This tool offers advanced schema analysis, validation, transformation, and visualization capabilities through a flexible command-line interface.

🌟 Features

• Schema Analysis

  • Generate schema summaries.
  • Detailed views of classes, slots, and types.
  • Support for hierarchical and section-based analysis.

• Schema Validation

  • Rigorous validation checks with detailed error reporting.
  • Optional metadata display for schemas.

• Schema Operations

  • Merge or concatenate multiple schemas.
  • Subset schemas by specified classes.

• Format Conversion

  • Export schemas to JSON, RDF, GraphQL, CSV, TSV, and SQL formats.
  • Customize RDF serialization formats (e.g., Turtle, XML).
  • SQL export supporting PostgreSQL, MySQL, SQLite, and DuckDB dialects.

• Visualization

  • Generate interactive HTML visualizations of schemas.
  • Options for inheritance, descriptions, and statistics display.

🚀 Installation

Using pip

pip install linkml-toolkit

Using conda

# Create environment from provided configuration
conda env create -f environment-dev.yml
conda activate linkml-toolkit-dev

# For production environment only
conda env create -f environment.yml
conda activate linkml-toolkit

Development Installation

# Clone the repository
git clone https://github.com/genomewalker/linkml-toolkit.git
cd linkml-toolkit

# Create and activate conda environment
conda env create -f environment-dev.yml
conda activate linkml-toolkit-dev

# Install in development mode
pip install -e ".[dev,test,docs]"

📚 Usage

Core Commands

Schema Summary

# Generate a summary of the schema
lmtk summary --schema schema.yaml

# Detailed view for specific sections
lmtk summary --schema schema.yaml --section slots --detailed

# Export summary to JSON
lmtk summary --schema schema.yaml --output summary.json

Schema Validation

# Validate schema
lmtk validate --schema schema.yaml

# Validate with metadata display
lmtk validate --schema schema.yaml --metadata

Schema Export

# Export to JSON Schema
lmtk export --schema schema.yaml --format json --output schema.json

# Export to RDF (Turtle format)
lmtk export --schema schema.yaml --format rdf --rdf-format turtle --output schema.ttl

# Export to SQL (PostgreSQL dialect)
lmtk export --schema schema.yaml --format sql --sql-dialect postgresql --output schema.sql

Schema Subset

# Create a subset containing specific classes
lmtk subset --schema schema.yaml --classes class1,class2 --output subset.yaml

# Exclude inherited elements
lmtk subset --schema schema.yaml --classes class1 --no-inherited --output subset.yaml

Schema Combination

# Merge schemas
lmtk combine --schema base.yaml --additional-schemas schema1.yaml -a schema2.yaml --mode merge --output merged.yaml

# Concatenate schemas
lmtk combine --schema base.yaml --additional-schemas schema1.yaml -a schema2.yaml --mode concat --output concatenated.yaml

Schema Visualization

# Generate an interactive HTML visualization
lmtk visualize --schema schema.yaml --output visualization.html

# Generate full documentation bundle
lmtk visualize --schema schema.yaml --output docs/ --full-docs

🛠️ Development

Environment Management

# Create development environment
conda env create -f environment.yml

# Update environment
conda env update -f environment.yml

# Create production environment
conda env create -f environment.prod.yml

Running Tests

# Run all tests
pytest

# Run with coverage
pytest --cov=linkml_toolkit

# Run specific test file
pytest tests/test_core.py

# Run tests with output
pytest -v

Building Documentation

# Build documentation
cd docs
mkdocs build

# Serve documentation locally
mkdocs serve

📖 Project Structure

linkml-toolkit/
├── src/
│   └── linkml_toolkit/      # Source code
├── tests/                   # Test suite
│   └── data/               # Test data
├── docs/                    # Documentation
├── environment.yml         # Development environment
├── environment.prod.yml    # Production environment
├── pyproject.toml         # Build configuration
├── setup.cfg              # Package metadata
└── tox.ini               # Test automation

🤝 Contributing

We welcome contributions! Here's how you can help:

1. Fork the Repository

   git clone https://github.com/genomewalker/linkml-toolkit.git
   cd linkml-toolkit

2. Set Up Development Environment

   conda env create -f environment.yml
   conda activate linkml-toolkit
   pip install -e ".[dev,test,docs]"

3. Create a Branch

   git checkout -b feature/your-feature-name

4. Make Changes

   • Write code
   • Add tests
   • Update documentation

5. Verify Changes

   # Run tests
   pytest
   
   # Run linting
   tox -e lint
   
   # Build docs
   cd docs && mkdocs build

6. Submit Pull Request

   • Push changes to your fork
   • Create pull request
   • Wait for review

📜 License

This project is licensed under the MIT License - see the LICENSE file for details.

🙏 Acknowledgments

• LinkML community for the base LinkML implementation.
• Contributors who have helped improve this toolkit.

📫 Contact

• Issue Tracker: GitHub Issues
• Documentation: ReadTheDocs