Fix NCI Trial API type error, update used GPT models, fix warnings and deprecations, Swift 6 language mode concurrency compatibility

NCIClinicalTrialsSearchAPI/OpenAPIClient/Classes/OpenAPIs/Extensions.swift

@@ -107,7 +107,7 @@ extension JSONEncodable where Self: Encodable {
     }
 }
 
-extension String: CodingKey {
+extension String: @retroactive CodingKey {
 
     public var stringValue: String {
         return self

NCIClinicalTrialsSearchAPI/OpenAPIClient/Classes/OpenAPIs/Models/StructuredEligibility.swift

@@ -21,9 +21,9 @@ public struct StructuredEligibility: Codable, JSONEncodable, Hashable {
     public var acceptsHealthyVolunteers: Bool?
     public var minAge: String?
     public var minAgeNumber: Int?
-    public var minAgeInYears: Int?
+    public var minAgeInYears: Double?
 
-    public init(maxAge: String? = nil, maxAgeNumber: Int? = nil, minAgeUnit: String? = nil, maxAgeUnit: String? = nil, maxAgeInYears: Int? = nil, gender: String? = nil, acceptsHealthyVolunteers: Bool? = nil, minAge: String? = nil, minAgeNumber: Int? = nil, minAgeInYears: Int? = nil) {
+    public init(maxAge: String? = nil, maxAgeNumber: Int? = nil, minAgeUnit: String? = nil, maxAgeUnit: String? = nil, maxAgeInYears: Int? = nil, gender: String? = nil, acceptsHealthyVolunteers: Bool? = nil, minAge: String? = nil, minAgeNumber: Int? = nil, minAgeInYears: Double? = nil) {
         self.maxAge = maxAge
         self.maxAgeNumber = maxAgeNumber
         self.minAgeUnit = minAgeUnit

NCIClinicalTrialsSearchAPI/OpenAPIClient/Classes/OpenAPIs/OpenISO8601DateFormatter.swift

@@ -8,7 +8,7 @@
 import Foundation
 
 // https://stackoverflow.com/a/50281094/976628
-public class OpenISO8601DateFormatter: DateFormatter {
+public class OpenISO8601DateFormatter: DateFormatter, @unchecked Sendable {
     static let withoutSeconds: DateFormatter = {
         let formatter = DateFormatter()
         formatter.calendar = Calendar(identifier: .iso8601)

NCIClinicalTrialsSearchAPI/docs/StructuredEligibility.md

@@ -12,7 +12,7 @@ Name | Type | Description | Notes
 **acceptsHealthyVolunteers** | **Bool** |  | [optional] 
 **minAge** | **String** |  | [optional] 
 **minAgeNumber** | **Int** |  | [optional] 
-**minAgeInYears** | **Int** |  | [optional] 
+**minAgeInYears** | **Double** |  | [optional] 
 
 [[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)
 

OwnYourData/ClinicalTrials/NCITrialsModule.swift

@@ -14,13 +14,13 @@ import SpeziLocation
 
 @Observable
 class NCITrialsModule: Module, EnvironmentAccessible {
-    @ObservationIgnored @Dependency private var locationModule: SpeziLocation
-    
+    @ObservationIgnored @Dependency(SpeziLocation.self) private var locationModule
+
     private let apiKey: String
     private(set) var trials: [TrialDetail] = []
     var zipCode: String = "10025"
-    var searchDistance: String = "100"
-    
+    var searchDistance: String = "50"  // Miles
+
 
     init(apiKey: String) {
         self.apiKey = apiKey

OwnYourData/ClinicalTrials/NICTrialsAPIDateFormatter.swift

@@ -12,7 +12,7 @@
 import Foundation
 
 
-class NICTrialsAPIDateFormatter: DateFormatter {
+class NICTrialsAPIDateFormatter: DateFormatter, @unchecked Sendable {
     static let withoutSeconds: DateFormatter = {
         let formatter = DateFormatter()
         formatter.calendar = Calendar(identifier: .iso8601)

OwnYourData/ClinicalTrials/TrialDetail+Identifiable.swift

@@ -9,7 +9,7 @@
 import OpenAPIClient
 
 
-extension TrialDetail: Identifiable {
+extension TrialDetail: @retroactive Identifiable {
     public var id: String? {
         self.nciId
     }

OwnYourData/Documents/PDFDocument+Transferable.swift

@@ -10,7 +10,7 @@ import PDFKit
 import SwiftUI
 
 
-extension PDFDocument: Transferable {
+extension PDFDocument: @retroactive Transferable {
     public static var transferRepresentation: some TransferRepresentation {
         DataRepresentation(
             contentType: .pdf,

OwnYourData/Helper/CodableArray+RawRepresentable.swift

@@ -9,7 +9,7 @@
 import Foundation
 
 
-extension Array: RawRepresentable where Element: Codable {
+extension Array: @retroactive RawRepresentable where Element: Codable {
     public var rawValue: String {
         guard let data = try? JSONEncoder().encode(self),
               let rawValue = String(data: data, encoding: .utf8) else {

OwnYourData/Home.swift

@@ -18,7 +18,7 @@ struct HomeView: View {
     }
 
     @Environment(Account.self) var account: Account?
-    @Environment(FHIRStore.self) var fjirStore
+    @Environment(FHIRStore.self) var fhirStore
 
     @State private var presentingAccount = false
     @State private var showMatchingView = false
@@ -34,7 +34,7 @@ struct HomeView: View {
                         .font(.system(size: 60).weight(.semibold))
                         .foregroundColor(.accentColor)
                         .multilineTextAlignment(.center)
-                    if fjirStore.llmRelevantResources.isEmpty {
+                    if fhirStore.llmRelevantResources.isEmpty {
                         InstructionsView()
                     }
                     OwnYourDataButton(title: "Match Me") {

OwnYourData/OwnYourDataDelegate.swift

@@ -25,6 +25,7 @@ import SwiftUI
 class OwnYourDataDelegate: SpeziAppDelegate {
     // See https://swiftpackageindex.com/stanfordspezi/spezi/documentation/spezi/speziappdelegate/configuration
     override var configuration: Configuration {
+        // swiftlint:disable:next closure_body_length
         Configuration(standard: OwnYourDataStandard()) {
             if !FeatureFlags.disableFirebase {
                 // See https://swiftpackageindex.com/stanfordspezi/speziaccount/documentation/speziaccount/initial-setup
@@ -64,8 +65,24 @@ class OwnYourDataDelegate: SpeziAppDelegate {
             LLMRunner {
                 LLMOpenAIPlatform(configuration: .init(concurrentStreams: 20, apiToken: self.openAIToken))
             }
-            FHIRInterpretationModule()
-
+            FHIRInterpretationModule(
+                summaryLLMSchema: LLMOpenAISchema(
+                    parameters: .init(
+                        modelType: .gpt4_o,
+                        systemPrompts: []
+                    )
+                ),
+                interpretationLLMSchema: LLMOpenAISchema(
+                    parameters: .init(
+                        modelType: .gpt4_o,
+                        systemPrompts: []
+                    )
+                ),
+                multipleResourceInterpretationOpenAIModel: .gpt4_o,
+                resourceCountLimit: 250,
+                allowedResourcesFunctionCallIdentifiers: nil
+            )
+
             DocumentManager()
 
             SpeziLocation()

OwnYourData/OwnYourDataStandard.swift

@@ -23,7 +23,7 @@
 import SwiftUI
 
 
-actor OwnYourDataStandard: Standard, EnvironmentAccessible, HealthKitConstraint, OnboardingConstraint, AccountStorageConstraint {
+actor OwnYourDataStandard: Standard, EnvironmentAccessible, HealthKitConstraint, ConsentConstraint, AccountStorageConstraint {
     enum OwnYourDataStandardError: Error {
         case userNotAuthenticatedYet
     }
@@ -32,8 +32,8 @@
         Firestore.firestore().collection("users")
     }
 
-    @Dependency var fhirStore: FHIRStore
-    @Dependency var accountStorage: FirestoreAccountStorage?
+    @Dependency(FHIRStore.self) var fhirStore
+    @Dependency(FirestoreAccountStorage.self) var accountStorage: FirestoreAccountStorage?
 
     @AccountReference var account: Account
 
@@ -106,39 +106,34 @@
 
     /// Stores the given consent form in the user's document directory with a unique timestamped filename.
     ///
-    /// - Parameter consent: The consent form's data to be stored as a `PDFDocument`.
-    func store(consent: PDFDocument) async {
-        let formatter = DateFormatter()
-        formatter.dateFormat = "yyyy-MM-dd_HHmmss"
-        let dateString = formatter.string(from: Date())
-
+    /// - Parameter consent: The consent form's data to be stored as a `SpeziOnboarding.ConsentDocumentExport`.
+    func store(consent: SpeziOnboarding.ConsentDocumentExport) async throws {
+        guard let consentData = await consent.pdf.dataRepresentation() else {
+            logger.error("Could not store consent form.")
+            return
+        }
+
         guard !FeatureFlags.disableFirebase else {
             guard let basePath = FileManager.default.urls(for: .documentDirectory, in: .userDomainMask).first else {
                 logger.error("Could not create path for writing consent form to user document directory.")
                 return
             }
-            
-            let filePath = basePath.appending(path: "consentForm_\(dateString).pdf")
-            consent.write(to: filePath)
-            
+
+            let filePath = await basePath.appending(path: "\(consent.documentIdentifier).pdf")
+            try consentData.write(to: filePath)
+
             return
         }
-        
+
         do {
-            guard let consentData = consent.dataRepresentation() else {
-                logger.error("Could not store consent form.")
-                return
-            }
-
             let metadata = StorageMetadata()
             metadata.contentType = "application/pdf"
-            _ = try await userBucketReference.child("consent/\(dateString).pdf").putDataAsync(consentData, metadata: metadata)
+            _ = try await userBucketReference.child("consent/\(consent.documentIdentifier).pdf").putDataAsync(consentData, metadata: metadata)
         } catch {
             logger.error("Could not store consent form: \(error)")
         }
     }
 
-
     func create(_ identifier: AdditionalRecordId, _ details: SignupDetails) async throws {
         guard let accountStorage else {
             preconditionFailure("Account Storage was requested although not enabled in current configuration.")

OwnYourData/Resources/Localizable.xcstrings

@@ -67,7 +67,7 @@
         "en" : {
           "stringUnit" : {
             "state" : "translated",
-            "value" : "Find National Cancer Institute supported trials.\n\nWe noticed that you haven't saved any health records on your phone yet.\n\nPlease follow the instructions to retrieve your health records: [Apple Support - View health records on your iPhone or iPod touch](https://support.apple.com/en-us/HT208680).\n\nYou can find a list of supported institutions at [Apple Support - Institutions that support health records on iPhone and iPod touch](https://platform.openai.com/account/api-keys).\n\nPlease ensure that OwnYourData has access to your health records in the Apple Health App. You can find these settings in the privacy section of your profile in Apple Health."
+            "value" : "Find National Cancer Institute supported trials.\n\nWe noticed that you haven’t saved any health records on your phone yet.\n\nPlease follow the instructions to retrieve your health records: [Apple Support - View health records on your iPhone or iPod touch](https://support.apple.com/en-us/HT208680).\n\nYou can find a list of supported institutions at [Apple Support - Institutions that support health records on iPhone and iPod touch](https://platform.openai.com/account/api-keys).\n\nPlease ensure that OwnYourData has access to your health records in the Apple Health App. You can find these settings in the privacy section of your profile in Apple Health."
           }
         }
       }
@@ -101,10 +101,24 @@
 
     },
     "Identifying best matching trials ..." : {
-
+      "localizations" : {
+        "en" : {
+          "stringUnit" : {
+            "state" : "translated",
+            "value" : "Identifying best matching trials …"
+          }
+        }
+      }
     },
     "Inspecting FHIR resources ..." : {
-
+      "localizations" : {
+        "en" : {
+          "stringUnit" : {
+            "state" : "translated",
+            "value" : "Inspecting FHIR resources …"
+          }
+        }
+      }
     },
     "Keyword Identification Prompt" : {
       "comment" : "Title of the keyword identification prompt."
@@ -113,7 +127,14 @@
 
     },
     "Learn More ..." : {
-
+      "localizations" : {
+        "en" : {
+          "stringUnit" : {
+            "state" : "translated",
+            "value" : "Learn More …"
+          }
+        }
+      }
     },
     "License Information" : {
 
@@ -164,7 +185,7 @@
         "en" : {
           "stringUnit" : {
             "state" : "translated",
-            "value" : "Your task is to identify a minimal set of distinct and unique keywords to conduct a trial search for a patient diagnosed with cancer. 
\nUtilize the \"get_resources\" function to access the patient's FHIR resources. \nThe generic patient information will be passed into this context after this prompt.\nUtilize the function call as often as needed until you have a comprehensive picture of the patient's health status and you feel confident that you can respond with a few distinct keywords for the NIC trials API search.
\nAvoid any generic terms like \"cancer\" and other elements that might appear in all trial descriptions.
Only try to provide 5 or less keywords.\nTry to be as concrete and as narrow as possible based on the relevant FHIR resources.\n
Do not engage in any conversation; only respond with a list of keywords separated by commas without any other context, introduction, or surrounding information. \nThe resulting strings will be parsed for further processing."
+            "value" : "Your task is to identify a minimal set of distinct and unique keywords to conduct a trial search for a patient diagnosed with cancer. 
\nUtilize the “get_resources” function to access the patient’s FHIR resources. \nThe generic patient information will be passed into this context after this prompt.\nUtilize the function call as often as needed until you have a comprehensive picture of the patient’s health status and you feel confident that you can respond with a few distinct keywords for the NIC trials API search.
\nAvoid any generic terms like “cancer” and other elements that might appear in all trial descriptions.
Only try to provide 5 or less keywords.\nTry to be as concrete and as narrow as possible based on the relevant FHIR resources.\n
Do not engage in any conversation; only respond with a list of keywords separated by commas without any other context, introduction, or surrounding information. \nThe resulting strings will be parsed for further processing."
           }
         }
       }
@@ -175,7 +196,7 @@
         "en" : {
           "stringUnit" : {
             "state" : "translated",
-            "value" : "Your task is to identify a set of matching trials for the patient diagnosed with cancer using the NCI trials API. 

You will be provided with a set of keywords identified in a previous run of an LLM based on the patient's FHIR health records.
\nYou can request any health records using the get_records function calling mechanisms. Utilize the function call as often as needed until you have a comprehensive picture of the patient's health status.

Utilize the get_trials function to retrieve information about the possible trials retrieved from the NCI API using the keywords identified in a previous run.
Ensure that the trial description and inclusion criteria match the patient's health records.
\nRespond with all trial identifiers that seem a good match.
The trial identifies must be separated by commas.\nIt is encouraged to return 3-5 possible matching trials to provide the patient some choice but ensure that the trials are matching the patient profile.
Only use the trial identifiers that are parameter options for the get_trials function; do not make up or combine trial identifiers.
\nDo not engage in any conversation; only respond with a list of identifiers separated by commas without any other context, introduction, or surrounding information. \nThe resulting identifiers will be parsed for further processing."
+            "value" : "Your task is to identify a set of matching trials for the patient diagnosed with cancer using the NCI trials API. 

You will be provided with a set of keywords identified in a previous run of an LLM based on the patient’s FHIR health records.
\nYou can request any health records using the get_records function calling mechanisms. Utilize the function call as often as needed until you have a comprehensive picture of the patient’s health status.

Utilize the get_trials function to retrieve information about the possible trials retrieved from the NCI API using the keywords identified in a previous run.
Ensure that the trial description and inclusion criteria match the patient’s health records.
\nRespond with all trial identifiers that seem a good match.
The trial identifies must be separated by commas.\nIt is encouraged to return 3-5 possible matching trials to provide the patient some choice but ensure that the trials are matching the patient profile.
Only use the trial identifiers that are parameter options for the get_trials function; do not make up or combine trial identifiers.
\nDo not engage in any conversation; only respond with a list of identifiers separated by commas without any other context, introduction, or surrounding information. \nThe resulting identifiers will be parsed for further processing."
           }
         }
       }
@@ -184,7 +205,14 @@
 
     },
     "Loading NCI trials based on FHIR resources ..." : {
-
+      "localizations" : {
+        "en" : {
+          "stringUnit" : {
+            "state" : "translated",
+            "value" : "Loading NCI trials based on FHIR resources …"
+          }
+        }
+      }
     },
     "Location Access" : {
 

OwnYourData/TrialsMatching/LLMFunctions/GetTrialsLLMFunction.swift

@@ -46,7 +46,7 @@
 
                         Title: \(trial.briefTitle ?? "") (\(trial.officialTitle ?? ""))
                         Description: \(trial.detailDescription ?? "")
-                        Incluision Criteria: \(trial.eligibility?.unstructured?.compactMap { $0.description }.joined() ?? "")
+                        Inclusion Criteria: \(trial.eligibility?.unstructured?.compactMap { $0.description }.joined() ?? "")
                         """
                     }
             }