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:
master branch is currently capable of parsing STU 3, v3.0.0.
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.
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).
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*.
fhir-parseras a submodule/subdirectory to the project that will use it
Create the file
mappings.pyin 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.pyto your liking by overriding the mappings you wish to change.
Similarly, create the file
settings.pyin 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.
Install the generator's requirements by running
pip3 install -r requirements.txt
Create a script that copies your
settings.pyfile to the root of
fhir-parser, _cd_s into
fhir-parserand then runs
generate.py. The generate script by default wants to use Python 3, issue
python generate.pyif you don't have Python 3 yet.
- Supply the
-fflag to force a re-download of the spec.
- Supply the
-c) flag to deny the re-download of the spec and only use cached resources (incompatible with
- Supply the
NOTE that the script currently overwrites existing files without asking and without regret.
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
To get a sense of how to use fhir-parser, take a look at these libraries:
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
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
- 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.