Mappings

Mapper module provides a way to convert data with arbitrary schema to FHIR resource(s) and store results in Aidbox.

Most of real-world healthcare applications are integrated with 3rd-party systems to ingest data from them. Using the Mapping resource, you can describe how 3rd-party data is being converted to the FHIR format. Mappings are written using the JUTE language.

The Mapping is an Aidbox resource, so all CRUD operations are applicable to it. The Mapping's schema is pretty straightforward:

resourceType: Mapping
id: mapping-id-here
body:
  # Executable part of the mapping written in the JUTE language (required)
scopeSchema:
  # A JSON schema for the incoming data (optional)

If the scopeSchema attribute is provided, incoming mapping data (also called a scope) will be validated against it first. Then, a JUTE template from the body will be executed. Mapping should return a valid Transaction Bundle, so when applied, it will be able to operate with multiple resources not just single one.

Example

Let's do a simple mapping which will create a Patient resource from the following data structure:

firstName: John
lastName: Smith
birthDate: 2000-01-02

The following request will create a mapping resource:

If you're not familiar with JUTE, please check out JUTE Tutorial to understand basic concepts.

PUT /Mapping/example
Content-Type: text/yaml

resourceType: Mapping
id: example
scopeSchema:
  # JSON schema describing incoming data structure
  type: object
  required: ["firstName", "lastName", "birthDate"]
  properties:
    firstName:
      type: string 
    lastName:
      type: string
    birthDate:
      type: string
      pattern: "^[0-9]{4}-[0-9]{2}-[0-9]{2}$"

body:
  # JUTE template which transforms incoming data to Transaction Bundle
  resourceType: Bundle
  type: transaction
  entry:
    - request:
        url: /fhir/Patient
        method: POST
      resource:
        resourceType: Patient
        birthDate: $ birthDate
        name:
          - given: ["$ firstName"]
            family: $ lastName

When a template is created, you can invoke the $apply operation on it to generate a Patient resource and save it into the database:

POST /Mapping/example/$apply
Content-Type: text/yaml

firstName: John
lastName: Smith
birthDate: '2010-12-12'

$apply Endpoint

To execute Mapping and store its result to the Aidbox database, do a POST request to the $apply endpoint. Request's body will be passed to a JUTE as an incoming data (scope):

POST /Mapping/<mapping-id>/$apply
Content-Type: application/json

{ "foo": 42, "bar": "hello" }

Make sure that your Mapping returns a Transaction Bundle, otherwise its result won't be persisted to a database.

$debug Endpoint

To check Mapping's result without actual persisting, you can do a POST request to the $debug endpoint:

POST /Mapping/<mapping-id>/$debug
Content-Type: text/yaml

foo: 42
bar: hello

Response will contain a mapping result or an error if evaluation failed for some reason.

Global $debug Endpoint

There is a way to check a mapping result without persisting it as a resource:

POST /Mapping/$debug
Content-Type: text/yaml

mapping:
  body:
    mul: $ 2 * foo
    str: $ "hello, " + name
    
  scopeSchema:
    type: object
    required: ["foo", "name"]
    properties:
      foo:
        type: integer
      name:
        type: string
    
scope:
  foo: 4
  name: "Bob"

You pass both Mapping and incoming data (scope) in a request body. Request response will contain the mapping result or an error information.

Including Mapping inside other Mapping

In Aidbox, there is the $include directive which allows you to include a Mapping within another one:

PUT /Mapping/index
Content-Type: text/yaml

resourceType: Mapping
id: index
body:
  $switch: $ type
  patient:
    $include: "patient"
  practitioner:
    $include: "practitioner"
  $default: null

This template will pass execution to either /Mapping/patient or /Mapping/practitioner depending on the value of the type key. Current evaluation scope will be passed to the included Mapping.

Because potentially there is a way to create an infinite recursion using the$include directive, there is an inclusion depth limit which equals to 5 for now.

Mapping Parameters

omit-drop-blanks parameter

Let's say we want to specify request depending on the gender field:

PATCH /Mapping/pat-example

body:
  entry:
    - request:
        url: $ '/Patient/' + patientId
        method: PATCH
      resource:
        resourceType: "Patient"
        gender:
          $if: $ gender
          $then: $ gender
          $else: null

JUTE will remove all empty values (nulls and empty arrays) and Aidbox will answer with "Please provide body for patch" response.

Passing omit-drop-blanks parameter will solve the issue.

PATCH /Mapping/pat-example

params:
  omit-drop-blanks: true
body:
  entry:
    - request:
        url: $ '/Patient/' + patientId
        method: PATCH
      resource:
        resourceType: "Patient"
        gender:
          $if: $ gender
          $then: $ gender
          $else: null

Mapping Editor in the Aidbox UI

There is a Mapping Editor in the Aidbox UI with a built-in syntax checker and Debug capabilities. Search for the "Mappings" item in the left navigation menu.