At the end of the building process you will be able to connect to the FHIR repository :
This portal was made by @diashenrique.
With some modification to handle Apple's activity footsteps.
The app will first request you to accept to share some information.
Click on authorize
Then you can test the FHIR server by clicking on 'Save and test server'
The default settings point to the docker configuration.
If succeed, you can enter your patient information.
First Name, Last Name, Birthday, Genre.
The save the patient to Fhir. A pop-up will show you your unique Fhir ID.
Consult this patient on the portal:
Go to: http://localhost:32783/fhir/portal/patientlist.html
We can see here, that there is a new patient "toto" with 0 activities.
Send her activities:
Go back to the iOS application and click on Step count
This panel summaries the step count of the week. In our case 2 entries.
Now you can send them to InterSystems IRIS FHIR by a click on send.
Consult the new activities on the portal:
We can see now that Toto has two new observation and activities.
You can event click on the chart button to display it as a chart.
Most of this demo is built on SwiftUI.
https://developer.apple.com/xcode/swiftui/
Who is the latest framework for iOS and co.
How to check for authorization for health data works It's in the SwiftFhirIrisManager class.
This class is a singleton and it will be carrying all around the application with @EnvironmentObject annotation.
More info at : https://www.hackingwithswift.com/quick-start/swiftui/how-to-use-environmentobject-to-share-data-between-views
The requestAuthorization method:
// Request authorization to access HealthKit.
func requestAuthorization( ) {
// Requesting authorization.
/// - Tag: RequestAuthorization
let writeDataTypes : Set < HKSampleType > = dataTypesToWrite ( )
let readDataTypes : Set < HKObjectType > = dataTypesToRead ( )
// requset authorization
healthStore. requestAuthorization ( toShare: writeDataTypes, read: readDataTypes) { ( success, error) in
if !success {
// Handle the error here.
} else {
DispatchQueue . main. async {
self . authorizedHK = true
}
}
}
} Where healthStore is the object of HKHealthStore().
The HKHealthStore is like the database of healthdata in iOS.
dataTypesToWrite and dataTypesToRead are the object we would like to query in the database.
The authorization need a purpose and this is done in the Info.plist xml file by adding:
<key >NSHealthClinicalHealthRecordsShareUsageDescription</key >
<string >Read data for IrisExporter</string >
<key >NSHealthShareUsageDescription</key >
<string >Send data to IRIS</string >
<key >NSHealthUpdateUsageDescription</key >
<string >Write date for IrisExporter</string >
How to connect to a FHIR Repository For this part I used the FHIR package from Smart-On-FHIR : https://github.com/smart-on-fhir/Swift-FHIR
The class used is the FHIROpenServer.
private func test( ) {
progress = true
let url = URL ( string: self . url)
swiftIrisManager. fhirServer = FHIROpenServer ( baseURL : url! , auth: nil )
swiftIrisManager. fhirServer. getCapabilityStatement ( ) { FHIRError in
progress = false
showingPopup = true
if FHIRError == nil {
showingSuccess = true
textSuccess = " Connected to the fhir repository "
} else {
textError = FHIRError ? . description ?? " Unknow error "
showingSuccess = false
}
return
}
} This create a new object fhirServer in the singleton swiftIrisManager.
Next we use the getCapabilityStatement()
If we can retrieve the capabilityStatement of the FHIR server this mean we successfully connected to the FHIR repository.
This repository is not in HTTPS, by default apple bock this kind of communication.
To allow HTTP support, the Info.plist xml file is edited like this:
<key >NSAppTransportSecurity</key >
<dict >
<key >NSExceptionDomains</key >
<dict >
<key >localhost</key >
<dict >
<key >NSIncludesSubdomains</key >
<true />
<key >NSExceptionAllowsInsecureHTTPLoads</key >
<true />
</dict >
</dict >
</dict >
How to save a patient in the FHIR Repository Basic operation by first checking if the patient already exists in the repository
Patient . search ( [ " family " : " \( self . lastName) " ] ) . perform ( fhirServer) This search for patient with the same family name.
Here we can imaging other scenarios like with Oauth2 and JWT token to join the patientid and his token. But for this demo we keep things simple.
Next if the patient exist, we retrieve it, otherwise we create the patient :
func createPatient( callback: @escaping ( Patient ? , Error ? ) -> Void ) {
// Create the new patient resource
let patient = Patient . createPatient ( given: firstName, family: lastName, dateOfBirth: birthDay, gender: gender)
patient? . create ( fhirServer, callback: { ( error) in
callback ( patient, error)
} )
}
How to extract data from the HealthKit
It's done by querying the healthkit Store (HKHealthStore())
Here we are querying for footsteps.
Prepare the query with the predicate.
//Last week
let startDate = swiftFhirIrisManager. startDate
//Now
let endDate = swiftFhirIrisManager. endDate
print ( " Collecting workouts between \( startDate) and \( endDate) " )
let predicate = HKQuery . predicateForSamples ( withStart: startDate, end: endDate, options: HKQueryOptions . strictEndDate) Then the query itself with his type of data (HKQuantityType.quantityType(forIdentifier: .stepCount)) and the predicate.
func queryStepCount( ) {
//Last week
let startDate = swiftFhirIrisManager. startDate
//Now
let endDate = swiftFhirIrisManager. endDate
print ( " Collecting workouts between \( startDate) and \( endDate) " )
let predicate = HKQuery . predicateForSamples ( withStart: startDate, end: endDate, options: HKQueryOptions . strictEndDate)
let query = HKSampleQuery ( sampleType: HKQuantityType . quantityType ( forIdentifier: . stepCount) !, predicate: predicate, limit: HKObjectQueryNoLimit, sortDescriptors: nil ) { ( query, results, error) in
guard let results = results as? [ HKQuantitySample ] else {
return
}
process ( results, type: . stepCount)
}
healthStore. execute ( query)
}
How to transform HealthKit data to FHIR For this part, we use the Microsoft package HealthKitToFHIR
https://github.com/microsoft/healthkit-to-fhir
This is a usefull package that offer factories to transform HKQuantitySample to FHIR Observation
let observation = try ! ObservationFactory ( ) . observation ( from: item)
let patientReference = try ! Reference ( json: [ " reference " : " Patient/ \( patientId) " ] )
observation. category = try ! [ CodeableConcept ( json: [
" coding " : [
[
" system " : " http://terminology.hl7.org/CodeSystem/observation-category " ,
" code " : " activity " ,
" display " : " Activity "
]
]
] ) ]
observation. subject = patientReference
observation. status = . final
print ( observation)
observation. create ( self . fhirServer, callback: { ( error) in
if error != nil {
completion ( error)
}
} ) Where item is an HKQuantitySample in our case a stepCount type.
The factory does most of the job of converting 'unit' and 'type' to FHIR codeableConcept and 'value' to FHIR valueQuantity.
The reference to the patientId is done manually by casting a json fhir reference.
let patientReference = try ! Reference ( json: [ " reference " : " Patient/ \( patientId) " ] ) Same is done for the category :
observation. category = try ! [ CodeableConcept ( json: [
" coding " : [
[
" system " : " http://terminology.hl7.org/CodeSystem/observation-category " ,
" code " : " activity " ,
" display " : " Activity "
]
]
] ) ] At last the observation is created in the fhir repository :
observation. create ( self . fhirServer, callback: { ( error) in
if error != nil {
completion ( error)
}
} )
Not much to say, it's based on the fhir template form the InterSystems community :
https://openexchange.intersystems.com/package/iris-fhir-template
It's based on Henrique works who is a nice front end for FHIR repositories made in jquery.
https://openexchange.intersystems.com/package/iris-fhir-portal
