Arno Kaimbacher
c049b22723
- fix: Update API routes to include DOI URL handling and improve route organization - chore: Add ORCID preload rule file and ensure proper registration - docs: Add MIT License to the project for open-source compliance - feat: Implement command to detect and fix missing dataset cross-references - feat: Create command for updating DataCite DOI records with detailed logging and error handling - docs: Add comprehensive documentation for dataset indexing command - docs: Create detailed documentation for DataCite update command with usage examples and error handling
205 lines
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5 KiB
Markdown
205 lines
No EOL
5 KiB
Markdown
# Tethys Research Repository Backend System
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Welcome to the Tethys Research Repository Backend System! This is the backend component responsible for managing datasets, users, and the core functionality of the Tethys Data Research Repository.
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## Table of Contents
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- [Getting Started](#getting-started)
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- [Prerequisites](#prerequisites)
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- [Installation](#installation)
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- [Usage](#usage)
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- [Configuration](#configuration)
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- [Database](#database)
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- [API Documentation](#api-documentation)
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- [Commands](#commands)
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- [Documentation](#documentation)
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- [Contributing](#contributing)
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- [License](#license)
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## Getting Started
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### Prerequisites
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Before you begin, ensure you have met the following requirements:
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- Node.js and npm installed on your development machine.
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- A running PostgreSQL database instance.
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- AdonisJS CLI globally installed.
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### Installation
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1. Clone this repository:
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```bash
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git clone git clone https://gitea.geologie.ac.at/geolba/tethys.backend.git
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cd tethys-backend
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```
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2. Install dependencies:
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```bash
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npm install
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```
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3. Configure environment variables (see [Configuration](#configuration))
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4. Run database migrations:
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```bash
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node ace migration:run
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```
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5. Start the development server:
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```bash
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npm run dev
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```
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## Usage
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The Tethys Backend provides RESTful APIs for managing research datasets, user authentication, DOI registration, and search functionality.
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## Configuration
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Copy the `.env.example` file to `.env` and configure the following variables:
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### Database Configuration
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```bash
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DB_CONNECTION=pg
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DB_HOST=localhost
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DB_PORT=5432
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DB_USER=your_username
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DB_PASSWORD=your_password
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DB_DATABASE=tethys_db
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```
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### DataCite Configuration
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```bash
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# DataCite Credentials
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DATACITE_USERNAME=your_datacite_username
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DATACITE_PASSWORD=your_datacite_password
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DATACITE_PREFIX=10.21388
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# Environment-specific API endpoints
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DATACITE_API_URL=https://api.test.datacite.org # Test environment
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DATACITE_SERVICE_URL=https://mds.test.datacite.org # Test MDS
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# For production:
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# DATACITE_API_URL=https://api.datacite.org
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# DATACITE_SERVICE_URL=https://mds.datacite.org
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```
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### OpenSearch Configuration
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```bash
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OPENSEARCH_HOST=localhost:9200
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```
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### Application Configuration
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```bash
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BASE_DOMAIN=tethys.at
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APP_KEY=your_app_key
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```
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## Database
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The system uses PostgreSQL with Lucid ORM. Key models include:
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- **Dataset**: Research dataset metadata
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- **DatasetIdentifier**: DOI and other identifiers for datasets
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- **User**: User management and authentication
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- **XmlCache**: Cached XML metadata
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Run migrations and seeders:
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```bash
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# Run migrations
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node ace migration:run
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# Run seeders (if available)
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node ace db:seed
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```
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## API Documentation
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API endpoints are available for:
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- Dataset management (`/api/datasets`)
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- User authentication (`/api/auth`)
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- DOI registration (`/api/doi`)
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- Search functionality (`/api/search`)
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*Detailed API documentation can be found in the `/docs/api` directory.*
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## Commands
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The system includes several Ace commands for maintenance and data management:
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### Dataset Indexing
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```bash
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# Index all published datasets to OpenSearch
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node ace index:datasets
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# Index a specific dataset
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node ace index:datasets --publish_id 123
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```
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### DataCite DOI Management
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```bash
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# Update DataCite records for modified datasets
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node ace update:datacite
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# Show detailed statistics for datasets needing updates
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node ace update:datacite --stats
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# Preview what would be updated (dry run)
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node ace update:datacite --dry-run
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# Force update all DOI records
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node ace update:datacite --force
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# Update a specific dataset
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node ace update:datacite --publish_id 123
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```
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*For detailed command documentation, see the [Commands Documentation](docs/commands/)*
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## Documentation
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Comprehensive documentation is available in the `/docs` directory:
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- **[Commands Documentation](docs/commands/)** - Detailed guides for Ace commands
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- [DataCite Update Command](docs/commands/update-datacite.md) - DOI synchronization and management
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- [Dataset Indexing Command](docs/commands/index-datasets.md) - Search index management
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- **[API Documentation](docs/api/)** - REST API endpoints and usage
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- **[Deployment Guide](docs/deployment/)** - Production deployment instructions
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- **[Configuration Guide](docs/configuration/)** - Environment setup and configuration options
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## Contributing
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1. Fork the repository
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2. Create a feature branch (`git checkout -b feature/amazing-feature`)
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3. Commit your changes (`git commit -m 'Add some amazing feature'`)
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4. Push to the branch (`git push origin feature/amazing-feature`)
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5. Open a Pull Request
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### Development Guidelines
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- Follow the existing code style and conventions
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- Write tests for new features
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- Update documentation for any API changes
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- Ensure all commands and migrations work properly
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### Testing Commands
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```bash
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# Run tests
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npm test
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# Test specific commands
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node ace update:datacite --dry-run --publish_id 123
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node ace index:datasets --publish_id 123
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```
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## License
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This project is licensed under the [MIT License](LICENSE). |