DbssertAPI

Version 1.0.0

Simple Python FastAPI service for querying CURIE metadata from a Dbssert DuckDB file.

This repository complements Dbssert and is part of the broader Tablassert ecosystem.

Usage

Set database path (required)

export DBSSERT_PATH=/path/to/dbssert.duckdb

Install dependencies (Nix shell)

nix develop

Run server

serve-api

Server starts on port 8052.

API Routes

Health check endpoint:

GET /health

Returns plain text ok.

Entity lookup endpoint:

GET /curies-with-ner?entity=<text>

Returns JSON (application/json) as a list of records, including:

• CURIE
• PREFERRED_NAME
• SYNONYM
• CATEGORY_NAME
• TAXON_ID

Canonical CURIE lookup endpoint:

GET /cannoical-curie-information?curie=<CURIE>

Returns JSON (application/json) as a list of records, including:

• CURIE
• PREFERRED_NAME
• CATEGORY_NAME
• TAXON_ID

Architecture

Single-file implementation in lib/dbssert_api/api.py:

1. FastAPI app (APP) - Declares all HTTP routes.
2. DuckDB query handlers - Open DBSSERT_PATH in read-only mode and query CURIE metadata.
3. serve_api() - Starts Uvicorn on 0.0.0.0:8052.

Development

Enter development shell:

nix develop

Run server locally:

serve-api

Contributors

Skye Lane Goetz

Gwênlyn Glusman