PHIR: PECOS High-level Intermediate Representation

phir models the PHIR specification as a Pydantic model. See our docs. Included is the tool phir-cli that provides validation and pretty printing on the command line.

Prerequisites

Python >=3.10

Installation

Just issue pip install phir to obtain the latest stable release.

phir CLI

The package includes a CLI for directly validating PHIR JSON files using the command line.

❯ phir-cli -h
usage: phir-cli [-h] [-s] [-v] [jsonfile]

Validates and pretty prints valid PHIR

positional arguments:
  jsonfile       json file to validate against PHIR spec

options:
  -h, --help     show this help message and exit
  -s, --schema   dump JSON schema of the PHIR model and exit
  -v, --version  show program's version number and exit

Development

Clone the repository and run:

python -m venv .venv
source .venv/bin/activate
pip install -U pip setuptools
pip install -r requirements.txt
pre-commit install

Then, install the project using:

pip install -e .

See Makefile for other useful commands.

Testing

Issue pytest from the root directory.