Harmonization Examples

A layered, self-checking set of examples for the harmonization framework — a tool for mapping varied source data onto a single, canonical schema with consistent column names and consistent values.

• Guide / docs site: https://bmir-radx.github.io/harmonization-examples/
• Examples: examples/

Each example maps a small, purpose-built input onto a canonical schema and verifies its output against a committed golden master, so the code you read is code that is known to work. The examples are layered: start with 01-hello-harmonization, which introduces the rule model, and work upward.

The rule model

A RuleSet is an ordered list of rules. Each rule maps one or more source columns to a single target column by running the value through a transformation — an ordered list of primitive operations.

Running an example

The examples run against the framework installed in the sibling repo's virtualenv. From the examples/ directory:

# Python interface (also runs the golden-master assertion):
../../harmonization-framework/venv/bin/python 01-hello-harmonization/run_python.py

# CLI interface:
bash 01-hello-harmonization/run_cli.sh

See examples/README.md for the full catalog and how the examples are structured.

Building the docs locally

pip install -r requirements-docs.txt
mkdocs serve

The site is also built and published to GitHub Pages on every push to main (see .github/workflows/docs.yml).