jps-controlled-vocabularies-rest-api 0.1.0

A lightweight REST service that exposes controlled vocabularies and terms over HTTP for programmatic retrieval and validation.

jps-controlled-vocabularies-rest-api

A lightweight REST service that exposes controlled vocabularies and terms over HTTP for programmatic retrieval and validation.

🚀 Overview

jps-controlled-vocabularies-rest-api is a FastAPI-based REST service designed to provide programmatic access to controlled vocabularies and terminology. It serves as a stable API layer for consuming vocabulary data from various backend sources including YAML files and PostgreSQL databases.

Key Features

• RESTful API - Clean, well-documented endpoints for vocabulary and term operations
• Pluggable Backends - Support for YAML files (built-in) and PostgreSQL (via plugin)
• Search & Validation - Full-text search across terms and value validation capabilities
• OpenAPI Documentation - Automatic Swagger UI and ReDoc documentation
• Container-Ready - Docker and docker-compose configurations included
• Type-Safe - Full type hints with Pydantic models
• Production-Ready - Health checks, structured logging, and graceful error handling

Use Cases

1. Frontend Integration - Provide drop-down values and definitions for UI components
2. Service Integration - Enable backend services to validate terminology consistently
3. Data Validation - ETL pipelines can validate data against controlled vocabularies
4. CI/CD Validation - Ensure vocabulary definitions are valid before deployment

Architecture

┌─────────────────┐
│   FastAPI App   │
│   (Routers)     │
└────────┬────────┘
         │
         ▼
┌────────────────────┐
│  VocabularyStore   │
│   (Abstraction)    │
└────────┬───────────┘
         │
    ┌────┴─────┐
    ▼          ▼
┌─────────┐  ┌──────────────┐
│ YAML    │  │ PostgreSQL   │
│ Store   │  │ Store        │
│ (Built) │  │ (Plugin)     │
└─────────┘  └──────────────┘

📦 Installation

Option 1: Install from PyPI (coming soon)

pip install jps-controlled-vocabularies-rest-api

Option 2: Install from Source

git clone https://github.com/jai-python3/jps-controlled-vocabularies-rest-api.git
cd jps-controlled-vocabularies-rest-api
pip install -e .

Option 3: Using Docker

docker-compose up -d

🚀 Quick Start

1. Configure Environment

cp .env.example .env
# Edit .env with your configuration

Minimal configuration for YAML backend:

VOCAB_BACKEND=yaml
VOCAB_YAML_PATH=./vocabularies

2. Prepare Vocabulary Files

Place your YAML vocabulary files in the vocabularies/ directory:

# vocabularies/my_vocab.yaml
vocabulary_id: my_vocabulary
schema_version: "1.0"
title: My Vocabulary
description: Example vocabulary

terms:
  - key: term1
    name: Term One
    description: First term
    metadata:
      allowed_values: ["value1", "value2", "value3"]

3. Run the Service

Using Python directly:

python -m jps_controlled_vocabularies_rest_api.main

Using Uvicorn:

uvicorn jps_controlled_vocabularies_rest_api.main:app --host 0.0.0.0 --port 8000

Using Docker:

docker-compose up

4. Access the API

• API Base: http://localhost:8000
• Swagger UI: http://localhost:8000/docs
• ReDoc: http://localhost:8000/redoc
• OpenAPI Spec: http://localhost:8000/openapi.json

📚 API Endpoints

Health & Readiness

• GET /healthz - Simple health check
• GET /readyz - Detailed readiness check with backend status

Vocabularies

• GET /v1/vocabularies - List all vocabularies
• GET /v1/vocabularies/{vocabulary_id} - Get vocabulary details
• GET /v1/vocabularies/{vocabulary_id}/terms - List terms (with pagination)
• GET /v1/vocabularies/{vocabulary_id}/terms/{term_key} - Get specific term

Search

• GET /v1/search?q={query} - Search terms across vocabularies
  • Optional: vocabulary_id - Filter by vocabulary
  • Optional: limit, offset - Pagination

Validation

• POST /v1/validate/value - Validate a value against a term
• POST /v1/validate/registry - Validate the entire registry

💡 Example Usage

List Vocabularies

curl http://localhost:8000/v1/vocabularies

Response:

[
  {
    "vocabulary_id": "workflow.system_terminology",
    "schema_version": "1.0",
    "title": "Workflow and System Terminology",
    "description": "Core terms used across JPSHealth EHR workflow services",
    "term_count": 4
  }
]

Get Vocabulary Details

curl http://localhost:8000/v1/vocabularies/workflow.system_terminology

Search Terms

curl "http://localhost:8000/v1/search?q=ready"

Validate a Value

curl -X POST http://localhost:8000/v1/validate/value \
  -H "Content-Type: application/json" \
  -d '{
    "vocabulary_id": "workflow.system_terminology",
    "term_key": "readiness_status",
    "value": "Almost Ready"
  }'

Response:

{
  "is_valid": true,
  "normalized_value": "Almost Ready",
  "reasons": ["Value is in the list of allowed values"],
  "allowed_values": ["Ready", "Almost Ready", "Not Ready"],
  "pattern": null
}

⚙️ Configuration

Environment Variables

Variable	Default	Description
VOCAB_BACKEND	yaml	Backend type: yaml or postgres
VOCAB_YAML_PATH	-	Path to YAML file or directory (required for yaml backend)
VOCAB_YAML_RELOAD	false	Enable hot-reload of YAML vocabularies
VOCAB_SEARCH_CASE_SENSITIVE	false	Case-sensitive search
UVICORN_HOST	0.0.0.0	Server host
UVICORN_PORT	8000	Server port
POSTGRES_DSN	-	PostgreSQL connection string (for postgres backend)
CORS_ALLOW_ORIGINS	-	Comma-separated list of allowed CORS origins
LOG_REQUEST_BODIES	false	Enable request body logging

PostgreSQL Backend

To use PostgreSQL backend (requires plugin):

1. Install the plugin:

pip install jps-controlled-vocabularies-postgresql

2. Configure environment:

VOCAB_BACKEND=postgres
POSTGRES_DSN=postgresql://user:pass@localhost:5432/dbname

🧪 Development

Setup Development Environment

# Install with dev dependencies
make install

# Or manually
pip install -e ".[dev]"

Run Tests

# Run all tests
make test

# Run with coverage
pytest --cov=src --cov-report=html

# Run specific test file
pytest tests/test_health.py

Code Quality

# Format code
make format

# Run linters
make lint

# Fix auto-fixable issues
make fix

# Type checking
mypy src/

Pre-commit Hooks

pre-commit install
pre-commit run --all-files

🐳 Docker Deployment

Build Image

docker build -t jps-vocab-api:latest .

Run Container

docker run -d \
  -p 8000:8000 \
  -e VOCAB_BACKEND=yaml \
  -e VOCAB_YAML_PATH=/app/vocabularies \
  -v $(pwd)/vocabularies:/app/vocabularies:ro \
  --name jps-vocab-api \
  jps-vocab-api:latest

Using Docker Compose

docker-compose up -d
docker-compose logs -f
docker-compose down

📖 Documentation

• Software Requirements Specification (SRS)
• Development SOP
• Release SOP

🤝 Contributing

Contributions are welcome! Please follow these steps:

1. Fork the repository
2. Create a feature branch (git checkout -b feature/amazing-feature)
3. Make your changes
4. Run tests and linters (make test && make lint)
5. Commit your changes (git commit -m 'Add amazing feature')
6. Push to the branch (git push origin feature/amazing-feature)
7. Open a Pull Request

📝 Changelog

See CHANGELOG.md for release history.

📜 License

MIT License © Jaideep Sundaram

See LICENSE for details.

🔗 Related Projects

• jps-controlled-vocabularies-utils - Core vocabulary utilities
• jps-controlled-vocabularies-postgresql - PostgreSQL backend plugin

📧 Contact

Jaideep Sundaram - [e-mail]

Project Link: https://github.com/jai-python3/jps-controlled-vocabularies-rest-api