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.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:
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'
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.
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.
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.
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.omit-drop-blanks parameterLet'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 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.
Last modified 4mo ago