midomtoolbox 0.3.0

Shape, convert, summarize and analyse MIDOM deidentification Protocols

MIDOM Toolbox

Shape, convert, summarize and analyse MIDOM deidentification Protocols.

⚠️ Major version 0. Not feature complete. Still testing out the interface

• Works with MIDOM Protocols (https://pypi.org/project/midom/)
• Converts to CTP scripts
• Generates summaries

installation

pip install midomtoolbox

usage

Working with Protocols

To take a MIDOM protocol json file and render to markup format:

from midom.components import Protocol    
from midomtoolbox.render.markdown import render_protocol

# load protocol
with open("/tmp/ctp_pipeline.json") as f:
    protocol = Protocol.model_validate_json(f.read())

# render
with open("/tmp/output.md", "w") as f:
    f.write(render_protocol(protocol))

Validation

TODO

Other examples

See /examples

FAQ

Why MIDOM and MIDOMToolbox? Why not just all MIDOM? MIDOM is about an Object Model; it is as implementation-agnostic as possible. It has some python implementations for convenience, for JSON serialization for example. But the value is mostly in the interfaces it describes. It should be light-weight to include in other python packages, keeping its own package dependencies minimal

MIDOMToolbox is a library that fully embraces python and provides tools for anything involving MIDOM objects. As a toolbox, it is free to have a large number of dependencies.