work-with-pysof

name	work-with-pysof
description	Work on pysof Python bindings for SQL-on-FHIR. Use for PyO3, maturin, Python package setup, pysof tests, Python APIs, PyPI publishing concerns, and any files under crates/pysof.

pysof

Use this when working in crates/pysof or changing Python bindings for SQL-on-FHIR.

pysof is excluded from default workspace builds. Root cargo build does not build it.

Installation

pip install pysof

Development Setup

cd crates/pysof
uv venv --python 3.11
uv sync --group dev
uv run maturin develop --release

# Verify
uv run python -c "import pysof; print(pysof.get_version()); print(pysof.get_supported_fhir_versions())"

Testing

cd crates/pysof
uv run pytest python-tests/ -v
cargo test

The Python suite has historically had 58 tests, and the Rust pysof suite has historically had 17 tests. Recheck counts from the current tree instead of relying on those numbers when reporting results.

Key API

import pysof

# Basic transformation
result = pysof.run_view_definition(view_definition, bundle, "csv")

# With options
result = pysof.run_view_definition_with_options(view, bundle, "json", limit=10, fhir_version="R4")

# Streaming large NDJSON files
for chunk in pysof.ChunkedProcessor(view, "patients.ndjson", chunk_size=500):
    process(chunk["rows"])

# File-to-file, most memory efficient
stats = pysof.process_ndjson_to_file(view, "input.ndjson", "output.csv", "csv")