FHIR Resources

Contents:

• FHIR Resources
  • Uses of FHIR Resources in Fhirbug
    • As return values of mapper.to_fhir()
    • As values for mapper Attributes
  • Creating resources
  • Ignore missing required Attributes
  • The base Resource class

Fhirbug uses fhir-parser to automatically parse the Fhir specification and generate classes for resources based on resource definitions. It’s an excellent tool that downloads the Resource Definition files from the official website of FHIR and generates classes automatically. For more details, check out the project’s repository.

Fhirbug comes with pre-generated classes for all FHIR Resources, which live inside fhirbug.Fhir.resources. You can generate your own resource classes based on a subset or extension of the default resource definitions but this is not currently covered by this documentation.

Uses of FHIR Resources in Fhirbug

As return values of mapper.to_fhir()

FHIR Resource classes are used when a mapper instance is converted to a FHIR Resource using .to_fhir().

Supposing we have defined a mapper for the Location resource, we could see the following:

>>> Location
mappings.Location
>>> location = Location.query.first()
<mappings.Location>
>>> location.to_fhir()
<fhirbug.Fhir.Resources.patient.Patient>

As values for mapper Attributes

FHIR Resources are also used as values for mapper attributes that are either references to other Resources, Backbone Elements or complex datatypes.

For example, let’s return back to the Location example. As we can see in the FHIR specification, the Location.address attribute is of type Address. This would mean something like this:

>>> location.Fhir.address
<fhirbug.Fhir.Resources.address.Address>
>>> location.Fhir.address.as_json()
{
    'use': 'work',
    'type': 'physical',
    [...]
}
>>> location.Fhir.address.use
'work'

Creating resources

You will be wanting to use the Resource classes to create return values for your mapper attributes.

The default way for creating resource instances is by passing a json object to the constructor:

>>> from fhirbug.Fhir.resources import Observation
>>> o = Observation({
...     'id': '2',
...     'status': 'final',
...     'code': {'coding': [{'code': '5', 'system': 'test'}]},
... })

As you can see, this may get a but verbose so there are several shortcuts to help with that.

Resource instances can be created:

• by passing a dict with the proper json structure as we already saw

• by passing the same values as keyword arguments:

  >>> o = Observation(
  ...     id='2', status='final', code={'coding': [{'code': '5', 'system': 'test'}]}
  ... )
  

• when an attribute’s type is a Backbone Element or a complex type, we can pass a resource:

  >>> from fhirbug.Fhir.resources import CodeableConcept
  >>> test_code = CodeableConcept(coding=[{'code': '5', 'system': 'test'}])
  >>> o = Observation(id='2', status='final', code=test_code)
  

• When an attribute has a cardinality larger than one, that is its values are part of an array, but we only want to pass one value, we can skip the array:

  >>> test_code = CodeableConcept(coding={'code': '5', 'system': 'test'})
  >>> o = Observation(id='2', status='final', code=test_code)
  

Fhirbug tries to make it as easy to create resources as possible by providing several shortcuts with the base contructor.

Ignore missing required Attributes

If you try to initialize a resource without providing a value for a required attribute you will get an error:

>>> o = Observation(id='2', status='final')
FHIRValidationError: {root}:
'Non-optional property "code" on <fhirbug.Fhir.Resources.observation.Observation object>
is missing'

You can suppress errors into warnings by passing the strict=False argument:

>>> o = Observation(id='2', status='final', strict=False)

Fhirbug will display a warning but it will not complain again if you try to save or serve the instance. It’s up to you make sure that your data is well defined.

The base Resource class

Tis is the abstract class used as a base to provide common functionality to all produced Resource classes. It has been modified in order to provide a convenient API for Creating resources.

class fhirbug.Fhir.base.fhirabstractbase.FHIRAbstractBase