kotobuki

kotobuki is a Python package that can update custom mappings created in Usagi that have become outdated in a new release of the OHDSI vocabularies.

Installation

kotobuki requires Python 3.11+ and is available on PyPI.

Depending on the type of database you have, you'll also need to install the required python adapter library. E.g. for postgresql, you can use psycopg2.

See SQLAlchemy docs for a list of supported dialects.

As kotobuki is intended to be used as a standalone tool, the recommended method of installation is in an isolated (temporary) environment.

E.g. if using uv with a postgresql database:

uvx --with psycopg2 --from kotobuki update-usagi-file --help

Or within a Jupyter notebook:

uv run --with jupyter,psycopg2,kotobuki jupyter lab

Usage

See User documentation

Contributing

We welcome all contributions, including bug reports, fixes, documentation enhancements, new ideas, and general improvements.

• We use the GitHub issue tracker for all bugs/issues/enhancements.
• See the contributing page for instructions on kotobuki development.