FHIR Zeug - A FHIR Spec Compiler

(forked from https://github.com/smart-on-fhir/fhir-parser)

Why a fork?

The original project seemed to abandoned and its structure was not quite pythonic. The work which has been done was great and we wanted to continue development here. We wanted to have a more self-contained project, which already has the definitions for the languages on board.

Our main support goals are Python (3.8) with pydantic and FHIR R4.

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

Usage

The fhir_zeug.cli module is the central CLI utility included. In an installed environment it can be called with

Make sure you have the ouput not in the project directory otherwise you will run into issues with poetry.

poetry run fhirzeug  --output-directory ../pydantic-fhir --generator python_pydantic

It will:

• Download the FHIR specification
• Parse it
• Generate
  • source files for python pydantic
  • a full python package also available (here)[https://pypi.org/project/pydantic-fhir/]).

Technical explanations

About ValueSets and CodeSystems

Article to understand the difference in FHIR between a ValueSets and a CodeSystems : https://fhir-drills.github.io/ValueSet-And-CodeSystem.html .

FHIR Specification provides different ways to define a ValueSet. At the moment, FHIRzeug implementation only handle a few cases :

• If a ValueSet is based on a single CodeSystem and this CodeSystem is defined in FHIR, then a DocEnum object is generated to validate this ValueSet.
  Example : ValueSet https://www.hl7.org/fhir/valueset-account-status.html is based on CodeSystem https://www.hl7.org/fhir/codesystem-account-status.html .
• If a ValueSet is based on a single CodeSystem but this CodeSystem is not included in the FHIR specification, FHIRzeug do not implement it as an Enum. If FHIR provides an exhaustive list of possible values (e.g. : under spec["compose"]["include"][0]["concept"]), ValueSet is validated by a typing.Literal. Warning : this is different from having access to the full CodeSystem. Especially, there is no documentation.
  Example : ValueSet https://www.hl7.org/fhir/valueset-duration-units.html .
• If a ValueSet is based on a single CodeSystem, this CodeSystem is not included in FHIR specification and the ValueSet is defined as a filter of the fields of the CodeSystem, no specific validation is implemented.
  Example : https://www.hl7.org/fhir/valueset-all-distance-units.html .
• If a ValueSet is based on several CodeSystems, no specific validation is implemented.

Note : when no specific validation is implemented, the attribute has the generic type FHIRCode which is a constrained string with the very permissive regex [^\s]+(\s[^\s]+)*.

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.

Maintained by:

and