python-fhir-converter 0.0.18

Transformation utility to translate data formats into FHIR

Python FHIR converter, fastish, most nuts and bolts included, ready for production

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Provides a python native version of FHIR-Converter written in C#.

The key features are:

• Fastish: Minimize overhead outside the rendering engine
• Move fast: Designed to be extensibile. Use the thin rendering API or leverage the builtin parts
• Easy: Designed to be easy to use, extend and deploy
• Robust: Get production-ready code

Limitations:

• Only CDA->FHIR is currently builtin. Additional work is needed to implement the filters, etc to support FHIR->FHIR and HL7v2->FHIR and back.
• Python-liquid requires a comma between parameters to filters. This does not appear to be a restriction with DotLiquid. As a result templates brought to this environment may need commas added.

Built on the back of:

• FHIR-Converter
• python-liquid

Table of Contents

• Install
• Links
• Basic Usage
• Command line interface
• Templates
• Benchmark
• Related Projects

Install

Install Python FHIR Converter using Pipenv:

$ pipenv install -u python-fhir-converter

Or pip:

$ pip install python-fhir-converter

Links

• PyPi: https://pypi.org/project/python-fhir-converter/
• Source Code: https://github.com/chaseastewart/fhir-converter
• Issue Tracker: https://github.com/chaseastewart/fhir-converter/issues

Basic Usage

See examples for more indepth usage / usecases.

from fhir_converter.renderers import  CcdaRenderer

with open("data/sample/ccda/ccd.ccda") as xml_in:
    print(CcdaRenderer().render_fhir_string("CCD", xml_in))

Command line interface

The package comes with a CLI interface that can be invoked either by the script name fhir_converter_cli or as python module python -m fhir_converter. The CLI allows you to transform a single file or an entire directory.

fhir_converter_cli  --from-file  ./data/sample/ccda/CCD.ccda --to-dir ./data/out --template-name CCD
---------------------------------------------------------------
RENDER SUCCESS
---------------------------------------------------------------
Total time: 0.14s
Finished at: 2024-01-11 10:49:44.182033
Final Memory: 32M
---------------------------------------------------------------

fhir-converter % fhir_converter_cli --template-dir ./data/templates/ccda --from-dir ./data/sample/ccda --to-dir ./data/out --template-name pampi
---------------------------------------------------------------
RENDER SUCCESS
---------------------------------------------------------------
Total time: 0.32s
Finished at: 2024-01-11 10:49:44.182033
Final Memory: 37M
---------------------------------------------------------------

Templates

Templates can be loaded from any python-liquid supported mechanism. To make packaging easier a ResourceLoader is provided. When a rendering environment is not provided, templates will be loaded from the module resources. To ease the creation of user defined templates a TemplateSystemLoader is provided that allows templates to be loaded from a primary and optionally default location. This allows user defined templates to reference templates in the default location. The example user defined templates reuse the default section / header templates.

Benchmark

You can run the benchmark from the root of the source tree. Test rig is a 16-inch, 2023 Macbook Pro with the M3 Pro not in low power mode. Python version is 3.12.1.

   Ordered by: cumulative time

   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
        3    0.000    0.000   12.273    4.091 ./scripts/benchmark.py:75(render_samples)
       22    0.003    0.000   12.272    0.558 ./fhir-converter/fhir_converter/renderers.py:187(render_files_to_dir)
      484    0.002    0.000   12.258    0.025 ./fhir-converter/fhir_converter/renderers.py:220(render_to_dir)
      484    0.010    0.000   12.172    0.025 ./fhir-converter/fhir_converter/renderers.py:93(render_fhir)
      484    0.003    0.000   12.004    0.025 ./fhir-converter/fhir_converter/renderers.py:117(render_to_fhir)

Related Projects

• FHIR-Converter
• python-liquid
• pyjson5
• xmltodict