SDRF Validator API

A FastAPI-based microservice for validating SDRF (Sample and Data Relationship Format) files against proteomics metadata standards.

Features

• File Upload Validation: Upload SDRF files (plain or gzipped) for validation
• Multiple Templates: Validate against various templates (human, vertebrates, plants, cell-lines, etc.)
• Multi-Template Validation: Validate against multiple templates simultaneously
• Ontology Validation: Optional validation of ontology terms against OLS
• RESTful API: Simple REST endpoints with OpenAPI documentation

API Endpoints

Method	Endpoint	Description
GET	/health	Health check
GET	/templates	List available validation templates
POST	/validate	Validate an uploaded SDRF file
POST	/validate/text	Validate SDRF content as text
GET	/docs	Swagger UI documentation
GET	/redoc	ReDoc documentation

Quick Start

Local Development

# Install dependencies
pip install -r requirements.txt

# Run the server
python app.py

# Or with uvicorn directly
uvicorn app:app --reload --port 5000

Docker

# Build and run with docker-compose
docker-compose up -d

# Or build manually
docker build -t sdrf-validator-api .
docker run -p 5000:5000 sdrf-validator-api

Kubernetes

Docker image is built and pushed to GitHub Container Registry (GHCR) by CI on push to main. Deploy the service and ingress once:

cd k8s
./deploy.sh

The deploy script applies deployment.yaml and ingress-pride-services.yaml (host www.ebi.ac.uk, path /pride/services/sdrf-validator). When a new image is pushed, rollout to pick it up:

kubectl rollout restart deployment/sdrf-validator -n sdrf-validator

Usage Examples

Validate an SDRF file

curl -X POST "http://localhost:5000/validate" \
  -F "file=@my_sdrf.tsv" \
  -F "template=default"

Validate with multiple templates

curl -X POST "http://localhost:5000/validate?template=default&template=human" \
  -F "file=@my_sdrf.tsv"

Validate gzipped file

curl -X POST "http://localhost:5000/validate" \
  -F "file=@my_sdrf.tsv.gz" \
  -F "template=default"

Get available templates

curl "http://localhost:5000/templates"

Python client example

import requests

# Upload and validate a file
with open("my_sdrf.tsv", "rb") as f:
    response = requests.post(
        "http://localhost:5000/validate",
        files={"file": f},
        params={"template": ["default", "human"], "skip_ontology": True}
    )

result = response.json()
print(f"Valid: {result['valid']}")
print(f"Errors: {result['error_count']}")
print(f"Warnings: {result['warning_count']}")

for error in result["errors"]:
    print(f"  ERROR: {error['message']}")

Available Templates

Template	Description
default / ms-proteomics	Standard mass spectrometry proteomics
human	Human-specific fields
vertebrates	Vertebrate organisms
invertebrates	Invertebrate organisms
plants	Plant-specific fields
cell-lines	Cell line experiments
base	Minimal required fields
single-cell	Single cell proteomics
immunopeptidomics	Immunopeptidomics experiments
metaproteomics	Metaproteomics experiments

Configuration

Environment variables:

Variable	Default	Description
PORT	5000	Server port
HOST	0.0.0.0	Server host
WORKERS	2	Number of uvicorn workers
LOG_LEVEL	INFO	Logging level
MAX_FILE_SIZE	10485760	Maximum file size in bytes (10MB)
CORS_ORIGINS	*	Allowed CORS origins (comma-separated)

Response Format

{
  "valid": false,
  "errors": [
    {
      "type": "ERROR",
      "message": "Missing required column: comment[data file]",
      "row": null,
      "column": null
    }
  ],
  "warnings": [
    {
      "type": "WARNING",
      "message": "Ontology term not found in EFO",
      "row": 2,
      "column": "characteristics[disease]"
    }
  ],
  "error_count": 1,
  "warning_count": 1,
  "templates_used": ["default"],
  "sdrf_pipelines_version": "0.0.34"
}

Development

Running Tests

pip install pytest httpx
pytest tests/ -v

Building Docker Image

docker build -t sdrf-validator-api:latest .

License

Apache 2.0