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A Python FHIR specification parser and class generator
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.gitignore Fixes for recent fhir changes (#17) May 4, 2018
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README.md
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fhirspec.py Introduce backwards compatibility for DSTU-2 codesystem/enum generati… Nov 20, 2019
fhirunittest.py Add enum generation capabilities, implement in Swift3 Nov 5, 2016
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requirements.txt REFACTORING: remove language implementations Feb 14, 2017

README.md

Python FHIR Parser

A Python FHIR specification parser for model class generation. If you've come here because you want Swift or Python classes for FHIR data models, look at our client libraries instead:

The master branch is currently capable of parsing STU 3, v3.0.0.
The develop branch should be capable of parsing the continuous integration build and will be merged into master on new major FHIR releases. There may be tags for specific freezes, see releases.

This work is licensed under the APACHE license. FHIR® is the registered trademark of HL7 and is used with the permission of HL7.

Tech

The generate.py script downloads FHIR specification files, parses the profiles (using fhirspec.py) and represents them as FHIRClass instances with FHIRClassProperty properties (found in fhirclass.py). Additionally, FHIRUnitTest (in fhirunittest.py) instances get created that can generate unit tests from provided FHIR examples. These representations are then used by Jinja templates to create classes in certain programming languages, mentioned below.

This script does its job for the most part, but it doesn't yet handle all FHIR peculiarities and there's no guarantee the output is correct or complete. This repository does not include the templates and base classes needed for class generation, you must do this yourself in your project. You will typically add this repo as a submodule to your framework project, create a directory that contains the necessary base classes and templates, create settings and mappings files and run the script. Examples on what you would need to do for Python classes can be found in Sample/settings.py, Sample/mappings.py and Sample/templates*.

Use

  1. Add fhir-parser as a submodule/subdirectory to the project that will use it

  2. Create the file mappings.py in your project, to be copied to fhir-parser root. First, import the default mappings using from Default.mappings import * (unless you will define all variables yourself anyway). Then adjust your mappings.py to your liking by overriding the mappings you wish to change.

  3. Similarly, create the file settings.py in your project. First, import the default settings using from Default.settings import * and override any settings you want to change. Then, import the mappings you have just created with from mappings import *. The default settings import the default mappings, so you may need to overwrite more keys from mappings than you'd first think. You most likely want to change the topmost settings found in the default file, which are determining where the templates can be found and generated classes will be copied to.

  4. Install the generator's requirements by running pip3 (or pip):

    pip3 install -r requirements.txt
  5. Create a script that copies your mappings.py and settings.py file to the root of fhir-parser, _cd_s into fhir-parser and then runs generate.py. The generate script by default wants to use Python 3, issue python generate.py if you don't have Python 3 yet.

    • Supply the -f flag to force a re-download of the spec.
    • Supply the --cache-only (-c) flag to deny the re-download of the spec and only use cached resources (incompatible with -f).

NOTE that the script currently overwrites existing files without asking and without regret.

Languages

This repo used to contain templates for Python and Swift classes, but these have been moved to the respective framework repositories. A very basic Python sample implementation is included in the Sample directory, complementing the default mapping and settings files in Default.

To get a sense of how to use fhir-parser, take a look at these libraries:

Tech Details

This parser still applies some tricks, stemming from the evolving nature of FHIR's profile definitions. Some tricks may have become obsolete and should be cleaned up.

How are property names determined?

Every “property” of a class, meaning every element in a profile snapshot, is represented as a FHIRStructureDefinitionElement instance. If an element itself defines a class, e.g. Patient.animal, calling the instance's as_properties() method returns a list of FHIRClassProperty instances – usually only one – that indicates a class was found in the profile. The class of this property is derived from element.type, which is expected to only contain one entry, in this matter:

  • If type is BackboneElement, a class name is constructed from the parent element (in this case Patient) and the property name (in this case animal), camel-cased (in this case PatientAnimal).
  • If type is *, a class for all classes found in settings star_expand_types` is created
  • Otherwise, the type is taken as-is (e.g. CodeableConcept) and mapped according to mappings' classmap, which is expected to be a valid FHIR class.

TODO: should http://hl7.org/fhir/StructureDefinition/structuredefinition-explicit-type-name be respected?

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