Fix Unknown Fields (#78)

# Fix Unknown Fields ## ♻️ Current situation & Problem - The viewer crashes if there is no heart rate or other information available for an ECG. ## ⚙️ Release Notes - Fix Unknown Fields ### Code of Conduct & Contributing Guidelines By submitting creating this pull request, you agree to follow our [Code of Conduct](https://github.com/StanfordBDHG/.github/blob/main/CODE_OF_CONDUCT.md) and [Contributing Guidelines](https://github.com/StanfordBDHG/.github/blob/main/CONTRIBUTING.md): - [x] I agree to follow the [Code of Conduct](https://github.com/StanfordBDHG/.github/blob/main/CODE_OF_CONDUCT.md) and [Contributing Guidelines](https://github.com/StanfordBDHG/.github/blob/main/CONTRIBUTING.md).
StanfordBDHG · Aug 26, 2024 · 56c6521 · 56c6521
1 parent 96136ad
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diff --git a/PAWS.xcodeproj/project.pbxproj b/PAWS.xcodeproj/project.pbxproj
@@ -16,6 +16,7 @@
 		2F65B44E2A3B8B0600A36932 /* NotificationPermissions.swift in Sources */ = {isa = PBXBuildFile; fileRef = 2F65B44D2A3B8B0600A36932 /* NotificationPermissions.swift */; };
 		2FA0BFED2ACC977500E0EF83 /* Localizable.xcstrings in Resources */ = {isa = PBXBuildFile; fileRef = 2FA0BFEC2ACC977500E0EF83 /* Localizable.xcstrings */; };
 		2FA25D492B8402A70016E4C7 /* HKElectrocardiogram+SupplementaryData.swift in Sources */ = {isa = PBXBuildFile; fileRef = 2FA25D482B8402A70016E4C7 /* HKElectrocardiogram+SupplementaryData.swift */; };
+		2FA7EC1C2C7C1CFB00D674AA /* FHIRTypes.swift in Sources */ = {isa = PBXBuildFile; fileRef = 2FA7EC1B2C7C1CFB00D674AA /* FHIRTypes.swift */; };
 		2FB099AF2A875DF100B20952 /* FirebaseAuth in Frameworks */ = {isa = PBXBuildFile; productRef = 2FB099AE2A875DF100B20952 /* FirebaseAuth */; };
 		2FB099B12A875DF100B20952 /* FirebaseFirestore in Frameworks */ = {isa = PBXBuildFile; productRef = 2FB099B02A875DF100B20952 /* FirebaseFirestore */; };
 		2FB099B32A875DF100B20952 /* FirebaseFirestoreSwift in Frameworks */ = {isa = PBXBuildFile; productRef = 2FB099B22A875DF100B20952 /* FirebaseFirestoreSwift */; };
@@ -110,6 +111,7 @@
 		2F65B44D2A3B8B0600A36932 /* NotificationPermissions.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = NotificationPermissions.swift; sourceTree = "<group>"; };
 		2FA0BFEC2ACC977500E0EF83 /* Localizable.xcstrings */ = {isa = PBXFileReference; lastKnownFileType = text.json.xcstrings; path = Localizable.xcstrings; sourceTree = "<group>"; };
 		2FA25D482B8402A70016E4C7 /* HKElectrocardiogram+SupplementaryData.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = "HKElectrocardiogram+SupplementaryData.swift"; sourceTree = "<group>"; };
+		2FA7EC1B2C7C1CFB00D674AA /* FHIRTypes.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = FHIRTypes.swift; sourceTree = "<group>"; };
 		2FAEC07F297F583900C11C42 /* PAWS.entitlements */ = {isa = PBXFileReference; lastKnownFileType = text.plist.entitlements; path = PAWS.entitlements; sourceTree = "<group>"; };
 		2FBF63322C2CF491002F4AC1 /* Firestore+User.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = "Firestore+User.swift"; sourceTree = "<group>"; };
 		2FC94CD4298B0A1D009C8209 /* PAWS.xctestplan */ = {isa = PBXFileReference; lastKnownFileType = text; path = PAWS.xctestplan; sourceTree = "<group>"; };
@@ -296,6 +298,7 @@
 				2FE5DC4429EDD7F2004B9AB4 /* CodableArray+RawRepresentable.swift */,
 				B2433E1C2BCF60C800D7C798 /* Contact+PersonNameComponents.swift */,
 				2FBF63322C2CF491002F4AC1 /* Firestore+User.swift */,
+				2FA7EC1B2C7C1CFB00D674AA /* FHIRTypes.swift */,
 			);
 			path = Helper;
 			sourceTree = "<group>";
@@ -418,8 +421,8 @@
 			buildRules = (
 			);
 			dependencies = (
+				2F15E22E2C7C3F6A006584DD /* PBXTargetDependency */,
 				2FDF443B2C65DB4A0075AFC1 /* PBXTargetDependency */,
-				2FDF443D2C65DB4A0075AFC1 /* PBXTargetDependency */,
 			);
 			name = PAWS;
 			packageProductDependencies = (
@@ -623,6 +626,7 @@
 				B2F7F1E22BA549A900BE93BE /* InvitationCodeError.swift in Sources */,
 				2FE5DC3629EDD7CA004B9AB4 /* HealthKitPermissions.swift in Sources */,
 				2F65B44E2A3B8B0600A36932 /* NotificationPermissions.swift in Sources */,
+				2FA7EC1C2C7C1CFB00D674AA /* FHIRTypes.swift in Sources */,
 				5661552E2AB854C000209B80 /* PackageHelper.swift in Sources */,
 				2FE5DC2629EDD38A004B9AB4 /* Contacts.swift in Sources */,
 				2FA25D492B8402A70016E4C7 /* HKElectrocardiogram+SupplementaryData.swift in Sources */,
@@ -651,13 +655,13 @@
 /* End PBXSourcesBuildPhase section */
 
 /* Begin PBXTargetDependency section */
-		2FDF443B2C65DB4A0075AFC1 /* PBXTargetDependency */ = {
+		2F15E22E2C7C3F6A006584DD /* PBXTargetDependency */ = {
 			isa = PBXTargetDependency;
-			productRef = 2FDF443A2C65DB4A0075AFC1 /* SwiftPackageListJSONPlugin */;
+			productRef = 2F15E22D2C7C3F6A006584DD /* SwiftLintPlugin */;
 		};
-		2FDF443D2C65DB4A0075AFC1 /* PBXTargetDependency */ = {
+		2FDF443B2C65DB4A0075AFC1 /* PBXTargetDependency */ = {
 			isa = PBXTargetDependency;
-			productRef = 2FDF443C2C65DB4A0075AFC1 /* SwiftLintPlugin */;
+			productRef = 2FDF443A2C65DB4A0075AFC1 /* SwiftPackageListJSONPlugin */;
 		};
 		653A255F28338800005D4D48 /* PBXTargetDependency */ = {
 			isa = PBXTargetDependency;
@@ -1024,7 +1028,7 @@
 			repositoryURL = "https://github.com/StanfordBDHG/HealthKitOnFHIR.git";
 			requirement = {
 				kind = upToNextMinorVersion;
-				minimumVersion = 0.2.7;
+				minimumVersion = 0.2.10;
 			};
 		};
 		2FCC1DCE2B6A2CE000C686BE /* XCRemoteSwiftPackageReference "SwiftLint" */ = {
@@ -1126,6 +1130,11 @@
 /* End XCRemoteSwiftPackageReference section */
 
 /* Begin XCSwiftPackageProductDependency section */
+		2F15E22D2C7C3F6A006584DD /* SwiftLintPlugin */ = {
+			isa = XCSwiftPackageProductDependency;
+			package = 2FCC1DCE2B6A2CE000C686BE /* XCRemoteSwiftPackageReference "SwiftLint" */;
+			productName = "plugin:SwiftLintPlugin";
+		};
 		2F3D4ABB2A4E7C290068FB2F /* SpeziScheduler */ = {
 			isa = XCSwiftPackageProductDependency;
 			package = 2F3D4ABA2A4E7C290068FB2F /* XCRemoteSwiftPackageReference "SpeziScheduler" */;
@@ -1165,11 +1174,6 @@
 			package = 5661551B2AB8384200209B80 /* XCRemoteSwiftPackageReference "swift-package-list" */;
 			productName = "plugin:SwiftPackageListJSONPlugin";
 		};
-		2FDF443C2C65DB4A0075AFC1 /* SwiftLintPlugin */ = {
-			isa = XCSwiftPackageProductDependency;
-			package = 2FCC1DCE2B6A2CE000C686BE /* XCRemoteSwiftPackageReference "SwiftLint" */;
-			productName = "plugin:SwiftLintPlugin";
-		};
 		2FE5DC6329EDD883004B9AB4 /* SpeziAccount */ = {
 			isa = XCSwiftPackageProductDependency;
 			package = 2FE5DC6229EDD883004B9AB4 /* XCRemoteSwiftPackageReference "SpeziAccount" */;

diff --git a/PAWS.xcodeproj/project.xcworkspace/xcshareddata/swiftpm/Package.resolved b/PAWS.xcodeproj/project.xcworkspace/xcshareddata/swiftpm/Package.resolved
@@ -105,8 +105,8 @@
       "kind" : "remoteSourceControl",
       "location" : "https://github.com/StanfordBDHG/HealthKitOnFHIR.git",
       "state" : {
-        "revision" : "b0cfe35a2263a517b22196b559d2dd1d1e2afcd9",
-        "version" : "0.2.9"
+        "revision" : "c24e316311ff9813cb1fe32cd8820bcca6e5e7f2",
+        "version" : "0.2.10"
       }
     },
     {

diff --git a/PAWS/ECGRecordings/ECGModule.swift b/PAWS/ECGRecordings/ECGModule.swift
@@ -9,19 +9,23 @@
 import FirebaseAuth
 import FirebaseFirestore
 import HealthKit
+import HealthKitOnFHIR
 import OSLog
-import enum ModelsR4.ResourceProxy
 import Spezi
 import SpeziFirebaseConfiguration
 import SpeziHealthKit
 import SpeziLocalStorage
 import UserNotifications
 
 
+@globalActor private actor ECGModuleActor: GlobalActor {
+    static let shared = ECGModuleActor()
+}
+
 @Observable
 class ECGModule: Module, DefaultInitializable, EnvironmentAccessible {
-    @ObservationIgnored @Dependency private var firebaseConfiguration: ConfigureFirebaseApp
-    @ObservationIgnored @Dependency private var healthKit: HealthKit
+    @ObservationIgnored @Dependency(ConfigureFirebaseApp.self) private var firebaseConfiguration
+    @ObservationIgnored @Dependency(HealthKit.self) private var healthKit
 
     private(set) var electrocardiograms: [HKElectrocardiogram] = []
     private var authStateDidChangeListenerHandle: AuthStateDidChangeListenerHandle?
@@ -48,13 +52,32 @@ class ECGModule: Module, DefaultInitializable, EnvironmentAccessible {
     func isUploaded(_ electrocardiogram: HKElectrocardiogram, reuploadIfNeeded: Bool = false) async throws -> Bool {
         let documentReference = try await Firestore.firestore().healthKitCollectionReference.document(electrocardiogram.uuid.uuidString)
         let snapshot = try await documentReference.getDocument()
-
-        guard !snapshot.exists else {
+
+        /// This function is intended to re-upload ECGs that have not been completely uploaded. Could be removed in the future.
+        func voltageComplete(_ electrocardiogramObservation: FHIRObservation) -> Bool {
+            guard let ecgCode = HKElectrocardiogramMapping.default.voltageMeasurements.codings.first else {
+                return false
+            }
+
+            // Unfortunately we have to support compiler with explicity type annotations on slower machines & the CI.
+            let voltageMeasurementsComponentsCount = electrocardiogramObservation.component?.filter { component in
+                component.code.coding?.contains(where: { coding in
+                    coding.code?.value?.string == ecgCode.code && coding.system?.value?.url == ecgCode.system
+                }) ?? false
+            }.count ?? 0
+
+            return voltageMeasurementsComponentsCount >= 3
+        }
+
+        if snapshot.exists,
+           let electrocardiogramObservation = try? snapshot.data(as: FHIRObservation.self),
+           voltageComplete(electrocardiogramObservation) {
             return true
         }
 
         if reuploadIfNeeded {
-            try await documentReference.setData(from: try electrocardiogram.resource)
+            await upload(electrocardiogram: electrocardiogram)
+            logger.log("Uploaded Missing ECG: \(electrocardiogram.id)")
             return true
         }
 
@@ -83,7 +106,7 @@ class ECGModule: Module, DefaultInitializable, EnvironmentAccessible {
         let samples = try await queryDescriptor.result(for: healthStore)
 
         self.electrocardiograms = samples
-        try await self.uploadUnuploadedECGs()
+        await self.uploadUnuploadedECGs()
     }
 
 
@@ -132,13 +155,15 @@ class ECGModule: Module, DefaultInitializable, EnvironmentAccessible {
         }
     }
 
+    @ECGModuleActor
     func remove(sample id: HKSample.ID) async throws {
         electrocardiograms.removeAll(where: { $0.uuid == id })
         try await Firestore.firestore().healthKitCollectionReference.document(id.uuidString).delete()
     }
 
 
     // MARK: - Private Helper Functions
+    @ECGModuleActor
     private func insert(electrocardiogram: HKElectrocardiogram) {
         electrocardiograms.removeAll(where: { $0.uuid == electrocardiogram.id })
         electrocardiograms.append(electrocardiogram)
@@ -181,9 +206,9 @@ class ECGModule: Module, DefaultInitializable, EnvironmentAccessible {
 
 
     private func upload(sample: HKSample, force: Bool = false) async throws {
-        let resource: ResourceProxy
+        let resource: FHIRResourceProxy
         if let electrocardiogram = sample as? HKElectrocardiogram {
-            self.insert(electrocardiogram: electrocardiogram)
+            await self.insert(electrocardiogram: electrocardiogram)
 
             guard try await !self.isUploaded(electrocardiogram) || force else {
                 return
@@ -192,7 +217,7 @@ class ECGModule: Module, DefaultInitializable, EnvironmentAccessible {
             async let symptoms = try electrocardiogram.symptoms(from: healthStore)
             async let voltageMeasurements = try electrocardiogram.voltageMeasurements(from: healthStore)
 
-            resource = ResourceProxy(
+            resource = FHIRResourceProxy(
                 with: try await electrocardiogram.observation(
                     symptoms: symptoms,
                     voltageMeasurements: voltageMeasurements
@@ -205,14 +230,14 @@ class ECGModule: Module, DefaultInitializable, EnvironmentAccessible {
         try await Firestore.firestore().healthKitCollectionReference.document(sample.id.uuidString).setData(from: resource)
     }
 
-    private func uploadUnuploadedECGs() async throws {
-        try await withThrowingTaskGroup(of: Void.self) { group in
-            for ecg in electrocardiograms where try await !isUploaded(ecg) {
+    private func uploadUnuploadedECGs() async {
+        await withTaskGroup(of: Void.self) { group in
+            for ecg in electrocardiograms {
                 group.addTask { [weak self] in
                     do {
                         try await self?.upload(sample: ecg)
                     } catch {
-                        self?.logger.log("Could not access HealthKit sample: \(error)")
+                        self?.logger.log("Could not upload ECG: \(error)")
                         await self?.addECGMessage(for: ecg, error: error)
                     }
                 }

diff --git a/PAWS/ECGRecordings/ECGRecording.swift b/PAWS/ECGRecordings/ECGRecording.swift
@@ -47,16 +47,16 @@ struct ECGRecording: View {
             }
             .padding()
         }
-        .task {
-            guard let symptoms = try? await electrocardiogram.symptoms(from: HKHealthStore()) else {
-                return
-            }
-
-            self.symptoms = symptoms
-
-            if !FeatureFlags.disableFirebase {
-                self.isUploaded = (try? await ecgModule.isUploaded(electrocardiogram, reuploadIfNeeded: true)) ?? false
+            .task {
+                guard let symptoms = try? await electrocardiogram.symptoms(from: HKHealthStore()) else {
+                    return
+                }
+
+                self.symptoms = symptoms
+
+                if !FeatureFlags.disableFirebase {
+                    self.isUploaded = (try? await ecgModule.isUploaded(electrocardiogram, reuploadIfNeeded: true)) ?? false
+                }
             }
-        }
     }
 }
diff --git a/PAWS/Helper/FHIRTypes.swift b/PAWS/Helper/FHIRTypes.swift
@@ -0,0 +1,15 @@
+//
+// This source file is part of the PAWS application based on the Stanford Spezi Template Application project
+//
+// SPDX-FileCopyrightText: 2023 Stanford University
+//
+// SPDX-License-Identifier: MIT
+//
+
+import ModelsR4
+
+
+typealias FHIRObservation = ModelsR4.Observation
+typealias FHIRResourceProxy = ModelsR4.ResourceProxy
+typealias FHIRObservationComponent = ModelsR4.ObservationComponent
+typealias FHIRCoding = ModelsR4.Coding
diff --git a/PAWS/PAWSStandard.swift b/PAWS/PAWSStandard.swift
@@ -10,7 +10,6 @@ import FirebaseAuth
 import FirebaseFirestore
 import FirebaseStorage
 import HealthKitOnFHIR
-import enum ModelsR4.ResourceProxy
 import OSLog
 import PDFKit
 import Spezi
@@ -24,9 +23,9 @@ import SwiftUI
 
 
 actor PAWSStandard: Standard, EnvironmentAccessible, HealthKitConstraint, OnboardingConstraint, AccountNotifyConstraint, AccountStorageConstraint {
-    @Dependency private var firebaseConfiguration: ConfigureFirebaseApp
-    @Dependency private var accountStorage: FirestoreAccountStorage?
-    @Dependency private var ecgStorage: ECGModule
+    @Dependency(ConfigureFirebaseApp.self) private var firebaseConfiguration
+    @Dependency(FirestoreAccountStorage.self) private var accountStorage: FirestoreAccountStorage?
+    @Dependency(ECGModule.self) private var ecgStorage
 
     private let logger = Logger(subsystem: "PAWS", category: "Standard")
 

diff --git a/PAWS/Study Information/EnrollmentGroup.swift b/PAWS/Study Information/EnrollmentGroup.swift
@@ -17,7 +17,7 @@ import SwiftUI
 
 @Observable
 class EnrollmentGroup: Module, EnvironmentAccessible {
-    @ObservationIgnored @Dependency private var configureFirebaseApp: ConfigureFirebaseApp
+    @ObservationIgnored @Dependency(ConfigureFirebaseApp.self) private var configureFirebaseApp
     private var dateOfBirth: Date?
     private var authStateDidChangeListenerHandle: AuthStateDidChangeListenerHandle?
     private var snapshotListener: ListenerRegistration?

diff --git a/README.md b/README.md
@@ -152,7 +152,7 @@ Copy the `ECGExporter` and `ECGReviewer` notebooks in Colab Enterprise, uncommen
 ## Continous Integration Setup
 
 The project supports different GitHub environments (`development`, `staging`, and `production`).
-- The Firebase proejct ID needs to be saved as a GitHub variable with the name `FIREBASE_PROJECT_ID` for the different deployment environments.
+- The Firebase project ID needs to be saved as a GitHub variable with the name `FIREBASE_PROJECT_ID` for the different deployment environments.
 - The service account key needs to be added to the GitHub secrets as `GOOGLE_APPLICATION_CREDENTIALS_BASE64` in a base64 encoding to enable the beta deployment.
 - To report code coverage, a CodeCov token should be added as a `CODECOV_TOKEN` environment secret.
 - The Firebase Google plist needs to be stored as a base64 encoded secret named `GOOGLE_SERVICE_INFO_PLIST_BASE64`.

diff --git a/ecg_data_manager/modules/visualization.py b/ecg_data_manager/modules/visualization.py
@@ -335,11 +335,21 @@ def plot_single_ecg(self, row):  # pylint: disable=too-many-locals
                 ax=axs[i],
             )
 
-        user_id = row[ColumnNames.USER_ID.value]
-        heart_rate = int(row[ColumnNames.HEART_RATE.value])
-        ecg_interpretation = row[
-            ColumnNames.APPLE_ELECTROCARDIOGRAM_CLASSIFICATION.value
-        ]
+        user_id = (
+            row[ColumnNames.USER_ID.value]
+            if row[ColumnNames.USER_ID.value] is not None
+            else "Unknown"
+        )
+        heart_rate = (
+            int(row[ColumnNames.HEART_RATE.value])
+            if row[ColumnNames.HEART_RATE.value] is not None
+            else "Unknown"
+        )
+        ecg_interpretation = (
+            row[ColumnNames.APPLE_ELECTROCARDIOGRAM_CLASSIFICATION.value]
+            if row[ColumnNames.APPLE_ELECTROCARDIOGRAM_CLASSIFICATION.value] is not None
+            else "Unknown"
+        )
 
         group_class = row[AGE_GROUP_STRING]
         user_id_html = widgets.HTML(
@@ -596,7 +606,6 @@ def save_diagnosis(  # pylint: disable=too-many-locals, too-many-arguments
                         "saved successfully.✓</span>"
                     )
                     display(data_saved_html)
-
                 else:
                     print(
                         "ECG has already been reviewed. No further review is required."
@@ -929,11 +938,21 @@ def plot_single_ecg(self, row):  # pylint: disable=too-many-locals
                 ax=axs[i],
             )
 
-        user_id = row[ColumnNames.USER_ID.value]
-        heart_rate = int(row[ColumnNames.HEART_RATE.value])
-        ecg_interpretation = row[
-            ColumnNames.APPLE_ELECTROCARDIOGRAM_CLASSIFICATION.value
-        ]
+        user_id = (
+            row[ColumnNames.USER_ID.value]
+            if row[ColumnNames.USER_ID.value] is not None
+            else "Unknown"
+        )
+        heart_rate = (
+            int(row[ColumnNames.HEART_RATE.value])
+            if row[ColumnNames.HEART_RATE.value] is not None
+            else "Unknown"
+        )
+        ecg_interpretation = (
+            row[ColumnNames.APPLE_ELECTROCARDIOGRAM_CLASSIFICATION.value]
+            if row[ColumnNames.APPLE_ELECTROCARDIOGRAM_CLASSIFICATION.value] is not None
+            else "Unknown"
+        )
 
         group_class = row[AGE_GROUP_STRING]
         user_id_html = widgets.HTML(

diff --git a/firebase/firebase-export-metadata.json b/firebase/firebase-export-metadata.json
@@ -1,16 +1,16 @@
 {
-  "version": "13.15.0",
+  "version": "13.15.4",
   "firestore": {
     "version": "1.19.7",
     "path": "firestore_export",
     "metadata_file": "firestore_export/firestore_export.overall_export_metadata"
   },
   "auth": {
-    "version": "13.15.0",
+    "version": "13.15.4",
     "path": "auth_export"
   },
   "storage": {
-    "version": "13.15.0",
+    "version": "13.15.4",
     "path": "storage_export"
   }
 }
diff --git a/firebase/firestore_export/all_namespaces/all_kinds/all_namespaces_all_kinds.export_metadata b/firebase/firestore_export/all_namespaces/all_kinds/all_namespaces_all_kinds.export_metadata