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StructureMap $extract

This $extract proof-of-concept reference implementation is an abstraction on top of an existing StructureMap $transform operation. We leveraged Brian Postlethwaite's .NET FHIR Mapping Language engine to expose a StructureMap $transform operation on https://proxy.smartforms.io/fhir/StructureMap/$transform.

note

This reference implementation is a proof-of-concept. It is highly likely that the underlying implementation will change in the future.

Deployed service: https://proxy.smartforms.io/fhir/QuestionnaireResponse/$extract

Underlying $transform service: https://proxy.smartforms.io/fhir/StructureMap/$transform

FHIR Mapping Language to StructureMap $convert service: https://proxy.smartforms.io/fhir/StructureMap/$convert

FHIR $extract operation definition: http://hl7.org/fhir/uv/sdc/OperationDefinition/QuestionnaireResponse-extract

FHIR $transform operation definition: https://hl7.org/fhir/r4/structuremap-operation-transform.html

FHIR Mapping Language $convert workflow: https://confluence.hl7.org/pages/viewpage.action?pageId=76158820#UsingtheFHIRMappingLanguage-WebServices

FHIR StructureMap-based extraction: https://hl7.org/fhir/uv/sdc/extraction.html#structuremap-based-extraction

Github: https://github.com/aehrc/smart-forms/tree/main/services/extract-express

Dockerhub: https://hub.docker.com/r/aehrc/smart-forms-extract

Usage​

Resource(s) can be extracted from a QuestionnaireResponse using a POST request to a URL such as:

https://proxy.smartforms.io/fhir/QuestionnaireResponse/$extract (type-level)

Parameters​

NameCardinalityTypeDocumentation
questionnaire-response1..1ResourceThe QuestionnaireResponse to extract data from. Used when the operation is invoked at the 'type' level.

Try it out​

Run In Postman

How it works​

The $extract operation is an abstraction on top of an existing StructureMap $transform operation.

The underlying $transform​

A $transform operation requires two input parameters:

  1. source - Contains the structure map defining the mapping rules
  2. content - Contains the data to be transformed (in terms of SDC, this is the QuestionnaireResponse)

The output of $transform is the transformed data, a FHIR resource.

Taking this logic, we can use a StructureMap $transform operation to perform the extraction of resources from a QuestionnaireResponse. Let's say we want to extract a bundle containing an Observation resource from a QuestionnaireResponse. We need a StructureMap that maps the data from the QuestionnaireResponse to the Observation resource. Normally we would write this mapping in FHIR Mapping Language and convert it to a StructureMap.

For more information on using the FHIR Mapping Language, refer to https://confluence.hl7.org/display/FHIR/Using+the+FHIR+Mapping+Language. Brian has a really awesome tool that can help you write and test your mappings at https://fhirpath-lab.com/FhirMapper2.

Once we have both the source StructureMap and the content QuestionnaireResponse, our $transform request body should look roughly like this:

{
  "resourceType": "Parameters",
  "parameter": [
    {
      "name": "source",
      "resource": //<insert StructureMap here> -
      }
    },
    {
      "name": "content",
      "resource": //<insert QuestionnaireResponse here> - a filled QR from
    }
  ]
}

Relevant resources:

source- https://smartforms.csiro.au/api/fhir/StructureMap/extract-bmi

content- http://smartforms.csiro.au/fhir/Questionnaire/CalculatedExpressionBMICalculatorPrepop

Running the $transform operation will return the transformed data, which in this case is a Bundle resource containing the Observation resource:

{
  "resourceType": "Bundle",
  "id": "<uuid>",
  "type": "transaction",
  "entry": [
    {
      "request": {
        "method": "POST",
        "url": "Observation"
      },
      "resource": {
        "resourceType": "Observation",
        "status": "final",
        "code": {
          "coding": [
            {
              "system": "http://snomed.info/sct",
              "code": "60621009",
              "display": "Body mass index"
            }
          ]
        },
        "subject": {
          "reference": "Patient/pat-sf"
        },
        "valueQuantity": {
          "value": 29.55,
          "unit": "kg/m2",
          "system": "http://unitsofmeasure.org",
          "code": "kg/m2"
        }
      }
    }
  ]
}

The $extract operation​

Using the logic above, we can abstract the $transform operation into a $extract operation. The $extract operation requires only one input parameter (or you can just provide the QuestionnaireResponse in the request body):

questionnaire-response - Contains the QuestionnaireResponse to extract data from

The provided QuestionnaireResponse should fulfill two criteria:

  1. It needs to contain a canonical reference in its questionnaire property.
{
  ...
  "questionnaire": "https://smartforms.csiro.au/docs/sdc/population/calculated-expression-1|0.1.0",
  ...
}
  1. The referenced Questionnaire should have a questionnaire-targetStructureMap extension. This extension needs to contain a canonical reference to a StructureMap that maps the data from the QuestionnaireResponse to the desired resource(s).
{
  ...
  "extension": [
    {
      "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-targetStructureMap",
      "valueCanonical": "https://smartforms.csiro.au/docs/StructureMap/extract-bmi"
    }
  ],
  ...
}

The $extract POC implementation defines a definitional repository to resolve Questionnaires and StructureMaps - https://smartforms.csiro.au/api/fhir. See https://hub.docker.com/r/aehrc/smart-forms-extract for more information.

The $extract operation will resolve the referenced Questionnaire + StructureMap, and set the StructureMap as the source in the $transform operation. The content will be the provided QuestionnaireResponse.

The underlying $transform operation will be executed, and the transformed data will be returned as the output of the $extract operation.

The $convert operation​

Brian's .NET FHIR Mapping Language engine has a handy debug mode that can be activated by adding debug=true to the $transform query parameters. The debug payload contains useful details such as warnings/errors, trace output, the converted StructureMap, and the output resource.

Conveniently, it also accepts both a FHIR Mapping Language map and a StructureMap resource as the source input. This means we can use it as a $convert operation to convert a FHIR Mapping Language map to a StructureMap resource.

https://proxy.smartforms.io/fhir/StructureMap/$convert

It expects the request headers for the Content-Type to be text/plain. The request body should contain the FHIR Mapping Language map, and the response will contain the converted StructureMap resource.

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