Add basic support for HKWorkout samples

.github/workflows/build-and-test.yml

@@ -23,18 +23,6 @@ jobs:
       artifactname: HealthKitOnFHIR.xcresult
       runsonlabels: '["macOS", "self-hosted"]'
       scheme: HealthKitOnFHIR
-  build:
-    name: Build for CodeQL & Swift 5.7
-    permissions:
-      contents: read
-      security-events: write
-    uses: StanfordBDHG/.github/.github/workflows/xcodebuild-or-fastlane.yml@v2
-    with:
-      runsonlabels: '["macos-13"]'
-      xcodeversion: 14.2.0
-      scheme: HealthKitOnFHIR
-      test: false
-      codeql: true
   buildandtestuitests:
     name: Build and Test UI Tests
     uses: StanfordBDHG/.github/.github/workflows/xcodebuild-or-fastlane.yml@v2

.github/workflows/pull-request.yml

@@ -19,3 +19,6 @@ jobs:
   swiftlint:
     name: SwiftLint
     uses: StanfordBDHG/.github/.github/workflows/swiftlint.yml@v2
+  markdown_link_check:
+    name: Markdown Link Check
+    uses: StanfordBDHG/.github/.github/workflows/markdown-link-check.yml@v2

README.md

@@ -46,7 +46,7 @@ let resource = try sample.resource
 
 ### Observations
 
-`HKQuantitySample`, `HKCategorySample`, `HKCorrelationSample`, and `HKElectrocardiogram` will be converted into FHIR [Observation](https://hl7.org/fhir/R4/observation.html) resources encapsulated in a [ResourceProxy](https://github.com/apple/FHIRModels/blob/main/HowTo/Instantiation.md#1-use-resourceproxy).
+`HKQuantitySample`, `HKCategorySample`, `HKCorrelationSample`, `HKElectrocardiogram`, and `HKWorkout` will be converted into FHIR [Observation](https://hl7.org/fhir/R4/observation.html) resources encapsulated in a [ResourceProxy](https://github.com/apple/FHIRModels/blob/main/HowTo/Instantiation.md#1-use-resourceproxy).
 
 ```swift
 let sample: HKQuantitySample = // ...

Sources/HealthKitOnFHIR/HKSampleMapping/HKElectrocardiogramMapping.swift

@@ -39,7 +39,7 @@ public struct HKElectrocardiogramMapping: Decodable {
     ///   - categories: The FHIR categories defined as ``MappedCode``s used for the specified `HKElectrocardiogram`
     ///   - classification: Defines the mapping of the `classification` category sample  of an `HKElectrocardiogram` to a FHIR observation.
     ///   - symptomsStatus: Defines the mapping of the `symptomsStatus` category sample  of an `HKElectrocardiogram` to a FHIR observation.
-    ///   - numberOfVoltageMeasurements: efines the mapping of the `numberOfVoltageMeasurements` quantity property of an `HKElectrocardiogram` to a FHIR observation.
+    ///   - numberOfVoltageMeasurements: Defines the mapping of the `numberOfVoltageMeasurements` quantity property of an `HKElectrocardiogram` to a FHIR observation.
     ///   - samplingFrequency: Defines the mapping of the `samplingFrequency` quantity property of an `HKElectrocardiogram` to a FHIR observation.
     ///   - averageHeartRate: Defines the mapping of the `averageHeartRate` quantity property of an `HKElectrocardiogram` to a FHIR observation.
     ///   - voltageMeasurements: Defines the mapping of the `voltageMeasurements` of an `HKElectrocardiogram` to a FHIR observation.

Sources/HealthKitOnFHIR/HKSampleMapping/HKQuantitySampleMapping.swift

@@ -23,7 +23,7 @@ public struct HKQuantitySampleMapping: Decodable {
     public var unit: MappedUnit
 
 
-    /// An ``HKQuantitySampleMapping`` allows developers to customize the mapping of `HKQuantitySample`s to an FHIR observations.
+    /// An ``HKQuantitySampleMapping`` allows developers to customize the mapping of `HKQuantitySample`s to FHIR observations.
     /// - Parameters:
     ///   - codings: The FHIR codings defined as ``MappedCode``s used for the specified `HKQuantitySample` type
     ///   - unit: The FHIR units defined as ``MappedUnit``s used for the specified `HKQuantitySample` type

Sources/HealthKitOnFHIR/HKSampleMapping/HKSampleMapping.swift

@@ -16,6 +16,7 @@ public struct HKSampleMapping: Decodable {
         case categorySampleMapping = "HKCategorySamples"
         case correlationMapping = "HKCorrelations"
         case electrocardiogramMapping = "HKElectrocardiogram"
+        case workoutSampleMapping = "HKWorkout"
     }
 
 
@@ -35,7 +36,9 @@ public struct HKSampleMapping: Decodable {
     public var correlationMapping: [HKCorrelationType: HKCorrelationMapping]
     /// The ``HKSampleMapping/electrocardiogramMapping`` property defines the mapping of  an`HKElectrocardiogramMapping` to a FHIR observation.
     public var electrocardiogramMapping: HKElectrocardiogramMapping
-
+    /// The ``HKSampleMapping/workoutMapping`` property defines the mapping of an `HKWorkout` to a FHIR Observation.
+    public var workoutSampleMapping: HKWorkoutSampleMapping
+
 
     public init(from decoder: Decoder) throws {
         let mappings = try decoder.container(keyedBy: CodingKeys.self)
@@ -82,12 +85,15 @@ public struct HKSampleMapping: Decodable {
         )
 
         let electrocardiogramMapping = try mappings.decode(HKElectrocardiogramMapping.self, forKey: .electrocardiogramMapping)
-
+
+        let workoutSampleMapping = try mappings.decode(HKWorkoutSampleMapping.self, forKey: .workoutSampleMapping)
+
         self.init(
             quantitySampleMapping: quantitySampleMapping,
             categorySampleMapping: categorySampleMapping,
             correlationMapping: correlationMapping,
-            electrocardiogramMapping: electrocardiogramMapping
+            electrocardiogramMapping: electrocardiogramMapping,
+            workoutSampleMapping: workoutSampleMapping
         )
     }
 
@@ -99,11 +105,13 @@ public struct HKSampleMapping: Decodable {
         quantitySampleMapping: [HKQuantityType: HKQuantitySampleMapping] = HKQuantitySampleMapping.default,
         categorySampleMapping: [HKCategoryType: HKCategorySampleMapping] = HKCategorySampleMapping.default,
         correlationMapping: [HKCorrelationType: HKCorrelationMapping] = HKCorrelationMapping.default,
-        electrocardiogramMapping: HKElectrocardiogramMapping = HKElectrocardiogramMapping.default
+        electrocardiogramMapping: HKElectrocardiogramMapping = HKElectrocardiogramMapping.default,
+        workoutSampleMapping: HKWorkoutSampleMapping = HKWorkoutSampleMapping.default
     ) {
         self.quantitySampleMapping = quantitySampleMapping
         self.categorySampleMapping = categorySampleMapping
         self.correlationMapping = correlationMapping
         self.electrocardiogramMapping = electrocardiogramMapping
+        self.workoutSampleMapping = workoutSampleMapping
     }
 }

Sources/HealthKitOnFHIR/HKSampleMapping/HKWorkoutSampleMapping.swift

@@ -0,0 +1,35 @@
+//
+// This source file is part of the HealthKitOnFHIR open source project
+//
+// SPDX-FileCopyrightText: 2023 Stanford University and the project authors (see CONTRIBUTORS.md)
+//
+// SPDX-License-Identifier: MIT
+//
+
+import HealthKit
+
+
+/// An ``HKWorkoutSampleMapping`` allows developers to customize the mapping of `HKWorkout` samples to FHIR Observations.
+public struct HKWorkoutSampleMapping: Decodable {
+    /// A default instance of an ``HKWorkoutSampleMapping`` allowing developers to customize the ``HKWorkoutSampleMapping``
+    /// The default values are loaded from the `HKSampleMapping.json` resource in the ``HealthKitOnFHIR`` Swift Package.
+    public static let `default` = HKSampleMapping.default.workoutSampleMapping
+
+    /// The FHIR codings defined as ``MappedCode``s to be used for `HKWorkout` samples
+    public var codings: [MappedCode]
+    /// The FHIR categories defined as ``MappedCode``s to be used for `HKWorkout` samples
+    public var categories: [MappedCode]
+
+
+    /// An ``HKWorkoutSampleMapping`` allows developers to customize the mapping of `HKWorkout`s to FHIR observations.
+    /// - Parameters:
+    ///   - codings: The FHIR codings defined as ``MappedCode``s used for the `HKWorkout` sample
+    ///   - categories: The FHIR categories defined as ``MappedCode``s used for the `HKWorkout` sample
+    public init(
+        codings: [MappedCode],
+        categories: [MappedCode]
+    ) {
+        self.codings = codings
+        self.categories = categories
+    }
+}

Sources/HealthKitOnFHIR/HealthKit Extensions/HKCategoryValue+String.swift

@@ -5,8 +5,10 @@
 //
 // SPDX-License-Identifier: MIT
 //
+
 import HealthKit
 
+
 protocol HKCategoryValueDescription: CustomStringConvertible {
     var categoryValueDescription: String { get throws }
 }

Sources/HealthKitOnFHIR/HealthKit Extensions/HKSample+ResourceProxy.swift

@@ -48,6 +48,8 @@ extension HKSample {
             try electrocardiogram.buildObservation(&observation, mappings: mapping)
         case let clinicalRecord as HKClinicalRecord:
             return try clinicalRecord.resource()
+        case let workout as HKWorkout:
+            try workout.buildWorkoutObservation(&observation)
         default:
             throw HealthKitOnFHIRError.notSupported
         }

Sources/HealthKitOnFHIR/HealthKit Extensions/HKSampleType+ResourceType.swift

@@ -12,7 +12,7 @@ import ModelsR4
 
 extension HKSampleType {
     /// Converts an `HKSampleType` into the corresponding FHIR resource type, defined as a `ResourceType`
-    public var resourceTyoe: ResourceType {
+    public var resourceType: ResourceType {
         get throws {
             switch self {
             case is HKQuantityType, is HKCorrelationType, is HKCategoryType:

Sources/HealthKitOnFHIR/HealthKit Extensions/HKWorkout+Observation.swift

@@ -0,0 +1,45 @@
+//
+// This source file is part of the HealthKitOnFHIR open source project
+//
+// SPDX-FileCopyrightText: 2023 Stanford University and the project authors (see CONTRIBUTORS.md)
+//
+// SPDX-License-Identifier: MIT
+//
+
+import HealthKit
+import ModelsR4
+
+
+extension HKWorkout {
+    /// Generates an observation that captures the type of physical activity performed for a single instance of physical activity, based on https://build.fhir.org/ig/HL7/physical-activity/StructureDefinition-pa-observation-activity-measure.html
+    /// Note:  An `HKWorkout` object can also act as a container for other `HKSample` objects, which will need to be converted to observations individually.
+    func buildWorkoutObservation(
+        _ observation: inout Observation,
+        mappings: HKSampleMapping = HKSampleMapping.default
+    ) throws {
+        let mapping = mappings.workoutSampleMapping
+
+        for code in mapping.codings {
+            observation.appendCoding(code.coding)
+        }
+
+        for category in mapping.categories {
+            observation.appendCategory(
+                CodeableConcept(coding: [category.coding])
+            )
+        }
+
+        let activityTypeString = self.workoutActivityType.description.asFHIRStringPrimitive()
+
+        let valueCodeableConcept = CodeableConcept(
+            coding: [
+                Coding(
+                    code: activityTypeString,
+                    system: "http://developer.apple.com/documentation/healthkit".asFHIRURIPrimitive()
+                )
+            ]
+        )
+
+        observation.value = .codeableConcept(valueCodeableConcept)
+    }
+}