ISA-JSON Data Steward

A desktop application and command-line toolkit for creating, validating, and managing ISA-JSON investigation metadata.

Features

• GUI Application — Desktop interface for managing ISA-JSON studies, assays, materials, and process sequences
• Batch Processing Pipeline — Automated conversion of experimental data to ISA-JSON format
• ISA-JSON Export — Generate compliant ISA-JSON files with full metadata
• Ontology Integration — Browse and link ontology terms to experimental metadata
• Template System — Configurable templates for assays, devices, materials, and protocols
• Validation — ISA-JSON schema validation and semantic checks

Requirements

• Python 3.11+

Installation

pip install -e ".[dev]"

Usage

GUI Application

python -m gui.main

CLI Tools

# Generate ISA-JSON from batch data
isa-json-steward-batch --data-root ./data --output-dir ./output

# Or using the module invocation
python -m utils.batch --data-root ./data --output-dir ./output

# Validate ISA-JSON files
python scripts/isa_json_validation.py path/to/file.json

Using Profiles

The application supports domain-specific profiles that customize templates, ontology references, and configuration:

# Load a profile
python -m gui.main --profile ./path/to/profile/

# Or set via environment variable
export ISA_STEWARD_PROFILE=./path/to/profile/

See the Profile Documentation for details on creating custom profiles.

Development

# Install dev dependencies
pip install -e ".[dev]"

# Run tests
pytest

# Run linting
pre-commit run --all-files

Project Structure

├── gui/              # Desktop GUI application
│   ├── dialogs/      # Dialog windows
│   ├── pages/        # Main application pages
│   ├── widgets/      # Reusable UI widgets
│   └── resources/    # Stylesheets and assets
├── utils/            # Core utilities
│   └── batch/        # Batch processing pipeline (run via `isa-json-steward-batch` or `python -m utils.batch`)
├── scripts/          # Standalone CLI tools
├── tests/            # Test suite
├── config/           # Default configuration
└── docs/             # Documentation

License

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

Contributing

See CONTRIBUTING.md for guidelines.