Adding Testing (#75)

# *Initial Tests*

## ♻️ Current situation & Problem
*Link any open issues or pull requests (PRs) related to this PR. Please
ensure that all non-trivial PRs are first tracked and discussed in an
existing GitHub issue or discussion.*


## ⚙️ Release Notes 
*Add a bullet point list summary of the feature and possible migration
guides if this is a breaking change so this section can be added to the
release notes.*
*Include code snippets that provide examples of the feature implemented
or links to the documentation if it appends or changes the public
interface.*


## 📚 Documentation
*Please ensure that you properly document any additions in conformance
to [Spezi Documentation
Guide](https://github.com/StanfordSpezi/.github/blob/main/DOCUMENTATIONGUIDE.md).*
*You can use this section to describe your solution, but we encourage
contributors to document your reasoning and changes using in-line
documentation.*


## ✅ Testing
*Please ensure that the PR meets the testing requirements set by CodeCov
and that new functionality is appropriately tested.*
*This section describes important information about the tests and why
some elements might not be testable.*


## 📝 Code of Conduct & Contributing Guidelines 

By submitting creating this pull request, you agree to follow our [Code
of
Conduct](https://github.com/CS342/.github/blob/main/CODE_OF_CONDUCT.md)
and [Contributing
Guidelines](https://github.com/CS342/.github/blob/main/CONTRIBUTING.md):
- [ ] I agree to follow the [Code of
Conduct](https://github.com/CS342/.github/blob/main/CODE_OF_CONDUCT.md)
and [Contributing
Guidelines](https://github.com/CS342/.github/blob/main/CONTRIBUTING.md).

Intake.xcodeproj/project.pbxproj

@@ -57,6 +57,7 @@
  2FF53D8B2A8725DE00042B76 /* SpeziMockWebService in Frameworks */ = {isa = PBXBuildFile; productRef = 2FF53D8A2A8725DE00042B76 /* SpeziMockWebService */; };
  2FF53D8D2A8729D600042B76 /* IntakeStandard.swift in Sources */ = {isa = PBXBuildFile; fileRef = 2FF53D8C2A8729D600042B76 /* IntakeStandard.swift */; };
  3C89F66D2B9D948B00A4F52D /* PatientInfo.swift in Sources */ = {isa = PBXBuildFile; fileRef = 3C89F66C2B9D948B00A4F52D /* PatientInfo.swift */; };
+ 510CAAF12BA0DFFB00872B1A /* MedicationTests.swift in Sources */ = {isa = PBXBuildFile; fileRef = 510CAAF02BA0DFFB00872B1A /* MedicationTests.swift */; };
  511827962B740192002033A0 /* SurgeryView.swift in Sources */ = {isa = PBXBuildFile; fileRef = 511827952B740191002033A0 /* SurgeryView.swift */; };
  51805C122B81853800D17109 /* IntakeMedication.swift in Sources */ = {isa = PBXBuildFile; fileRef = 51805C112B81853700D17109 /* IntakeMedication.swift */; };
  51805C152B81857100D17109 /* IntakeMedicationViewModel.swift in Sources */ = {isa = PBXBuildFile; fileRef = 51805C142B81857100D17109 /* IntakeMedicationViewModel.swift */; };
@@ -180,6 +181,7 @@
  2FE5DCAC29EE6107004B9AB4 /* AccountOnboarding.swift */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.swift; path = AccountOnboarding.swift; sourceTree = "<group>"; };
  2FF53D8C2A8729D600042B76 /* IntakeStandard.swift */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.swift; path = IntakeStandard.swift; sourceTree = "<group>"; };
  3C89F66C2B9D948B00A4F52D /* PatientInfo.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = PatientInfo.swift; sourceTree = "<group>"; };
+ 510CAAF02BA0DFFB00872B1A /* MedicationTests.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = MedicationTests.swift; sourceTree = "<group>"; };
  511827952B740191002033A0 /* SurgeryView.swift */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.swift; path = SurgeryView.swift; sourceTree = "<group>"; };
  51805C112B81853700D17109 /* IntakeMedication.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = IntakeMedication.swift; sourceTree = "<group>"; };
  51805C142B81857100D17109 /* IntakeMedicationViewModel.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = IntakeMedicationViewModel.swift; sourceTree = "<group>"; };
@@ -560,6 +562,7 @@
  isa = PBXGroup;
  children = (
  2F4E237D2989A2FE0013F3D9 /* LaunchTests.swift */,
+ 510CAAF02BA0DFFB00872B1A /* MedicationTests.swift */,
  );
  path = IntakeUITests;
  sourceTree = "<group>";
@@ -928,6 +931,7 @@
  isa = PBXSourcesBuildPhase;
  buildActionMask = 2147483647;
  files = (
+ 510CAAF12BA0DFFB00872B1A /* MedicationTests.swift in Sources */,
  2F4E237E2989A2FE0013F3D9 /* LaunchTests.swift in Sources */,
  );
  runOnlyForDeploymentPostprocessing = 0;

Intake.xcodeproj/xcshareddata/xcschemes/Intake.xcscheme

@@ -81,6 +81,14 @@
  argument = "--disableFirebase"
  isEnabled = "YES">
  </CommandLineArgument>
+ <CommandLineArgument
+ argument = "--skipToScrollable"
+ isEnabled = "NO">
+ </CommandLineArgument>
+ <CommandLineArgument
+ argument = "--testPatient"
+ isEnabled = "NO">
+ </CommandLineArgument>
  <CommandLineArgument
  argument = "--showOnboarding"
  isEnabled = "NO">
@@ -93,6 +101,10 @@
  argument = "--testSchedule"
  isEnabled = "NO">
  </CommandLineArgument>
+ <CommandLineArgument
+ argument = "--testMedication"
+ isEnabled = "NO">
+ </CommandLineArgument>
  <CommandLineArgument
  argument = "--useFirebaseEmulator"
  isEnabled = "NO">

Intake/Allergy Records/AllergyLLMAssistant.swift

@@ -68,6 +68,7 @@ struct UpdateAllergyFunction: LLMFunction {
  }
 }
 
+// The AllergyLLMAssistant allows the user to ask the chat questions about their current allergies and add new allergies to their data.
 struct AllergyLLMAssistant: View {
  @Environment(DataStore.self) private var data
  @Environment(NavigationPathWrapper.self) private var navigationPath

Intake/Home.swift

@@ -32,7 +32,11 @@ struct StartButton: View {
 
  var body: some View {
  Button(action: {
- navigationPath.append(NavigationViews.general)
+ if FeatureFlags.testMedication {
+ navigationPath.append(NavigationViews.medication)
+ } else {
+ navigationPath.append(NavigationViews.general)
+ }
  }) {
  Text("Create New Form")
  .font(.headline)

Intake/IntakeTestingSetup.swift

@@ -5,11 +5,14 @@
 //
 // SPDX-License-Identifier: MIT
 //
-
+import ModelsR4
+import SpeziFHIR
+import SpeziFHIRMockPatients
 import SwiftUI
 
 private struct IntakeAppTestingSetup: ViewModifier {
  @AppStorage(StorageKeys.onboardingFlowComplete) var completedOnboardingFlow = false
+ @Environment(FHIRStore.self) private var store
 
  func body(content: Content) -> some View {
  content
@@ -20,6 +23,11 @@ private struct IntakeAppTestingSetup: ViewModifier {
  if FeatureFlags.showOnboarding {
  completedOnboardingFlow = false
  }
+ if FeatureFlags.testPatient {
+ let bundle = await ModelsR4.Bundle.gonzalo160Duenas839
+ store.removeAllResources()
+ store.load(bundle: bundle)
+ }
  }
  }
 }

Intake/Medication View/IntakeDosage.swift

@@ -15,6 +15,7 @@
 import Foundation
 import SpeziMedication
 
+// The IntakeDosage struct has a localizedDescription that describes the dosage information.
 struct IntakeDosage: Dosage, Codable {
  var localizedDescription: String
 }

Intake/Medication View/IntakeMedication.swift

@@ -15,6 +15,7 @@
 import Foundation
 import SpeziMedication
 
+// This describes the IntakeMedication struct which contains a localizedDescription (medication name) and a list of dosages.
 struct IntakeMedication: Medication, Comparable, Codable {
  var localizedDescription: String
  var dosages: [IntakeDosage]

Intake/Medication View/IntakeMedicationInstance.swift

@@ -15,6 +15,7 @@
 import Foundation
 import SpeziMedication
 
+// This defines an IntakeMedicationInstance which is composed of an id, an IntakeMedication type, a dosage, and a schedule. 
 struct IntakeMedicationInstance: MedicationInstance, MedicationInstanceInitializable, Codable {
  let id: UUID
  let type: IntakeMedication

Intake/Medication View/IntakeMedicationViewModel.swift

@@ -19,6 +19,7 @@ import SpeziFHIR
 import SpeziMedication
 import SwiftUI
 
+// The IntakeMedicationSettingsViewModel takes the patient's FHIRStore medications and adds any that match to the medicationOptions to the medicationInstances list which is then used for the MedicationContentView.
 @Observable
 class IntakeMedicationSettingsViewModel: Module, MedicationSettingsViewModel, CustomStringConvertible {
  var medicationInstances: Set<IntakeMedicationInstance> = []
@@ -46,7 +47,9 @@ class IntakeMedicationSettingsViewModel: Module, MedicationSettingsViewModel, Cu
  .joined(separator: ", ")
  }
 
+ // The init is modified from the SpeziMedication examples to load in the existing patient medications from their FHIRStore data.
  init(existingMedications: [FHIRResource]) { // swiftlint:disable:this function_body_length
+ // medicationOptions provides the list of medications options chosen as the most common medications from the sample patients
  self.medicationOptions = [
  IntakeMedication(
  localizedDescription: "Hydrochlorothiazide 25 MG Oral Tablet",
@@ -99,17 +102,20 @@ class IntakeMedicationSettingsViewModel: Module, MedicationSettingsViewModel, Cu
  ]
 
  var foundMedications: [IntakeMedicationInstance] = []
+ // This function matches any patient medication from FHIRStore to a medication in medicationOptions.
  if !existingMedications.isEmpty {
  for medication in existingMedications {
  for option in medicationOptions where option.localizedDescription == medication.displayName {
  var medSchedule: SpeziMedication.Schedule
  let medRequest = medicationRequest(resource: medication)
  if case .boolean(let asNeeded) = medRequest?.dosageInstruction?.first?.asNeeded {
+ // Checks if medication is asNeeded, otherwise finds the frequency in days.
  if let asNeededbool = asNeeded.value?.bool {
  if asNeededbool {
  medSchedule = SpeziMedication.Schedule(frequency: .asNeeded)
  } else {
  let intValue: Int
+ // Need to convert from FHIRDecimal to int.
  let interval = medRequest?.dosageInstruction?.first?.timing?.repeat?.period?.value?.decimal
  if let interval = interval {
  intValue = interval.int
@@ -122,7 +128,7 @@ class IntakeMedicationSettingsViewModel: Module, MedicationSettingsViewModel, Cu
  guard let firstDosage = option.dosages.first else {
  continue
  }
-
+ // Create an IntakeMedicationInstance to the data. 
  let intakeMedicationInstance = IntakeMedicationInstance(
  type: option,
  dosage: firstDosage,
@@ -139,7 +145,8 @@ class IntakeMedicationSettingsViewModel: Module, MedicationSettingsViewModel, Cu
  func persist(medicationInstances: Set<IntakeMedicationInstance>) async throws {
  self.medicationInstances = medicationInstances
  }
-
+
+ // Converts a FHIRResource into a MedicationRequest.
  func medicationRequest(resource: FHIRResource) -> MedicationRequest? {
  guard case let .r4(resource) = resource.versionedResource,
  let medicationRequest = resource as? ModelsR4.MedicationRequest else {
@@ -149,6 +156,7 @@ class IntakeMedicationSettingsViewModel: Module, MedicationSettingsViewModel, Cu
  }
 }
 
+// Needed to convert the FHIRDecimal into an Int.
 extension Decimal {
  var int: Int {
  let intVal = NSDecimalNumber(decimal: self).intValue // swiftlint:disable:this legacy_objc_type

Intake/Medication View/MedicationContentView.swift

@@ -17,38 +17,49 @@ import SpeziFHIR
 import SpeziMedication
 import SwiftUI
 
+// This view displays the medications in the patient's FHIR data, and allows them to add, update and delete their medications.
 struct MedicationContentView: View {
  @Environment(FHIRStore.self) private var fhirStore
  @Environment(NavigationPathWrapper.self) private var navigationPath
  @Environment(DataStore.self) private var data
  @State private var presentSettings = false
-
+ 
  @State private var medicationSettingsViewModel: IntakeMedicationSettingsViewModel?
-
+ 
  var body: some View {
  VStack {
  if let medicationSettingsViewModel {
  MedicationSettings(allowEmptySave: true, medicationSettingsViewModel: medicationSettingsViewModel) {
- data.medicationData = medicationSettingsViewModel.medicationInstances
- navigationPath.path.append(NavigationViews.allergies)
+ if FeatureFlags.skipToScrollable {
+ data.medicationData = medicationSettingsViewModel.medicationInstances
+ navigationPath.path.append(NavigationViews.pdfs)
+ } else {
+ data.medicationData = medicationSettingsViewModel.medicationInstances
+ navigationPath.path.append(NavigationViews.allergies)
+ }
  }
-  .navigationTitle("Medications")
-  .navigationBarItems(trailing: NavigationLink(destination: MedicationLLMAssistant(presentingAccount: .constant(false))) {
-  Text("Chat")
-  })
+ .navigationTitle("Medications")
+ .navigationBarItems(trailing: NavigationLink(destination: MedicationLLMAssistant(presentingAccount: .constant(false))) {
+ Text("Chat")
+ })
  } else {
  ProgressView()
  }
  }
- .task {
- let patientMedications = fhirStore.llmMedications
- self.medicationSettingsViewModel = IntakeMedicationSettingsViewModel(existingMedications: patientMedications)
- var initialData: Set<IntakeMedicationInstance> = []
- if let newMed = self.medicationSettingsViewModel?.medicationInstances {
- initialData = newMed
- }
- data.medicationData = initialData
+ // Updates the medicationSettingsViewModel init if there's a change to the patient's fhirStore medications.
+ .onChange(of: fhirStore.llmMedications) {
+ medicationSettingsViewModel = .init(existingMedications: fhirStore.llmMedications)
+ }
+ // Task to initialize the MedicationSettingsViewModel with the patient's existing fhirStore medications.
+ .task {
+ let patientMedications = fhirStore.llmMedications
+ self.medicationSettingsViewModel = IntakeMedicationSettingsViewModel(existingMedications: patientMedications)
+ var initialData: Set<IntakeMedicationInstance> = []
+ if let newMed = self.medicationSettingsViewModel?.medicationInstances {
+ initialData = newMed
  }
+ data.medicationData = initialData
+ }
  }
 
  init() {}

Intake/Medication View/MedicationLLMAssistant.swift

@@ -18,6 +18,7 @@ import SpeziLLMLocal
 import SpeziLLMOpenAI
 import SwiftUI
 
+// Adds the current patient medications to the system prompt.
 func getCurrentPatientMedications(medicationList: Set<IntakeMedicationInstance>) -> String? {
  var medicationDetails = "The patient is currently taking several medications:"
  print(medicationList)
@@ -31,6 +32,7 @@ func getCurrentPatientMedications(medicationList: Set<IntakeMedicationInstance>)
  return medicationDetails.isEmpty ? nil : medicationDetails
 }
 
+// Provides medication LLM assistant functionality to allow the patient to ask about their current medications.
 struct MedicationLLMAssistant: View {
  @Environment(DataStore.self) private var data
  @Environment(NavigationPathWrapper.self) private var navigationPath

Intake/SharedContext/FeatureFlags.swift

@@ -23,4 +23,7 @@ enum FeatureFlags {
  #endif
  /// Adds a test task to the schedule at the current time
  static let testSchedule = CommandLine.arguments.contains("--testSchedule")
+ static let testPatient = CommandLine.arguments.contains("--testPatient")
+ static let testMedication = CommandLine.arguments.contains("--testMedication")
+ static let skipToScrollable = CommandLine.arguments.contains("--skipToScrollable")
 }

IntakeUITests/MedicationTests.swift

@@ -0,0 +1,54 @@
+//
+// MedicationTests.swift
+// IntakeUITests
+//
+// Created by Kate Callon on 3/12/24.
+//
+//
+// This source file is part of the Intake based on the Stanford Spezi Template Application project
+//
+// SPDX-FileCopyrightText: 2023 Stanford University
+//
+// SPDX-License-Identifier: MIT
+//
+
+import Foundation
+import XCTest
+
+class MedicationTests: XCTestCase {
+ override func setUpWithError() throws {
+ try super.setUpWithError()
+
+ continueAfterFailure = false
+
+ let app = XCUIApplication()
+ app.launchArguments = ["--skipOnboarding", "--disableFirebase", "--testPatient", "--testMedication", "--skipToScrollable"]
+ app.launch()
+ }
+
+ func testMedications() throws {
+ let app = XCUIApplication()
+
+ // Small workaround to wait until the madications loaded into main memory
+ sleep(8)
+
+ XCTAssertEqual(app.state, .runningForeground)
+ app.buttons["Create New Form"].tap()
+
+ XCTAssertTrue(app.staticTexts["Hydrochlorothiazide 25 MG Oral Tablet"].waitForExistence(timeout: 10))
+ XCTAssertTrue(app.staticTexts["amLODIPine 2.5 MG Oral Tablet"].waitForExistence(timeout: 10))
+ XCTAssertTrue(app.navigationBars["Medication Settings"].buttons["Add New Medication"].waitForExistence(timeout: 2))
+ XCTAssertTrue(app.navigationBars["Medication Settings"].buttons["Chat"].waitForExistence(timeout: 2))
+ app.navigationBars["Medication Settings"].buttons["Add New Medication"].tap()
+ app.buttons["Verapamil Hydrochloride 40 MG"].tap()
+ app.buttons["Save Dosage"].tap()
+ app.buttons["Add Medication"].tap()
+ XCTAssertTrue(app.staticTexts["Verapamil Hydrochloride 40 MG"].waitForExistence(timeout: 5))
+ app.buttons["Save Medications"].tap()
+ XCTAssertTrue(app.navigationBars["Patient Form"].waitForExistence(timeout: 2))
+// XCTAssertTrue(app.staticTexts["Hydrochlorothiazide 25 MG Oral Tablet"].waitForExistence(timeout: 5))
+// XCTAssertTrue(app.staticTexts["amLODIPine 2.5 MG Oral Tablet"].waitForExistence(timeout: 5))
+// XCTAssertTrue(app.staticTexts["Verapamil Hydrochloride 40 MG"].waitForExistence(timeout: 5))
+// XCTAssertTrue(app.staticTexts["2.5 MG - Every Day"].waitForExistence(timeout: 5))
+ }
+}