FHIR 0.5.2 and Improved Resource Handling (#39)

# FHIR 0.5.2 and Improved Resource Handling ## ⚙️ Release Notes - Update to Spezi FHIR 0.5.2 and all included improvements: https://github.com/StanfordSpezi/SpeziFHIR/releases/tag/0.5.2 - Display the data in the overview - Improve the resource selection and reenable the resource limit - Improve the prompts and resource selection ### 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 · Nov 26, 2023 · a24b5bc · a24b5bc
1 parent ee231da
commit a24b5bc
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Showing 11 changed files with 107 additions and 21 deletions.
diff --git a/LLMonFHIR.xcodeproj/project.pbxproj b/LLMonFHIR.xcodeproj/project.pbxproj
@@ -1110,7 +1110,7 @@
 			repositoryURL = "https://github.com/StanfordSpezi/SpeziFHIR.git";
 			requirement = {
 				kind = upToNextMinorVersion;
-				minimumVersion = 0.5.0;
+				minimumVersion = 0.5.2;
 			};
 		};
 		2F49B7742980407B00BCB272 /* XCRemoteSwiftPackageReference "Spezi" */ = {

diff --git a/LLMonFHIR.xcodeproj/project.xcworkspace/xcshareddata/swiftpm/Package.resolved b/LLMonFHIR.xcodeproj/project.xcworkspace/xcshareddata/swiftpm/Package.resolved
@@ -41,8 +41,8 @@
       "kind" : "remoteSourceControl",
       "location" : "https://github.com/StanfordSpezi/SpeziFHIR.git",
       "state" : {
-        "revision" : "786cf34055340aeb887265781aab5703bd685359",
-        "version" : "0.5.1"
+        "revision" : "d60882bf6f91f2719f33d413e22d1fc3e6f32705",
+        "version" : "0.5.2"
       }
     },
     {

diff --git a/LLMonFHIR/FHIR Display/InspectResourceView.swift b/LLMonFHIR/FHIR Display/InspectResourceView.swift
@@ -45,13 +45,25 @@ struct InspectResourceView: View {
                     Spacer()
                 }
             } else if let summary = fhirResourceSummary.cachedSummary(forResource: resource) {
-                Text(summary)
-                    .multilineTextAlignment(.leading)
-                    .contextMenu {
-                        Button("FHIR_RESOURCES_SUMMARY_BUTTON") {
-                            loadSummary(forceReload: true)
-                        }
+                VStack {
+                    HStack(spacing: 0) {
+                        Text(summary.title)
+                            .font(.title2)
+                            .multilineTextAlignment(.leading)
+                            .bold()
+                        Spacer()
                     }
+                    HStack(spacing: 0) {
+                        Text(summary.summary)
+                            .multilineTextAlignment(.leading)
+                            .contextMenu {
+                                Button("FHIR_RESOURCES_SUMMARY_BUTTON") {
+                                    loadSummary(forceReload: true)
+                                }
+                            }
+                        Spacer()
+                    }
+                }
             } else {
                 Button("FHIR_RESOURCES_SUMMARY_BUTTON") {
                     loadSummary()

diff --git a/LLMonFHIR/FHIR Interpretation/FHIRMultipleResourceInterpreter.swift b/LLMonFHIR/FHIR Interpretation/FHIRMultipleResourceInterpreter.swift
@@ -141,7 +141,7 @@ class FHIRMultipleResourceInterpreter {
 
                 switch functionCall.name {
                 case LLMFunction.getResourcesName:
-                    callGetResources(functionCall: functionCall)
+                    try await callGetResources(functionCall: functionCall)
                 default:
                     break
                 }
@@ -150,7 +150,7 @@ class FHIRMultipleResourceInterpreter {
     }
 
 
-    private func callGetResources(functionCall: LLMStreamResult.FunctionCall) {
+    private func callGetResources(functionCall: LLMStreamResult.FunctionCall) async throws {
         struct Response: Codable {
             let resources: String
         }
@@ -165,12 +165,21 @@ class FHIRMultipleResourceInterpreter {
         print("Parsed Resources: \(requestedResources)")
 
         for requestedResource in requestedResources {
-            for resource in fhirStore.allResources.filter({ $0.functionCallIdentifier == requestedResource }) {
+            var fittingResources = fhirStore.allResources.filter { $0.functionCallIdentifier == requestedResource }
+            print("Fitting Resources: \(fittingResources.count)")
+            if fittingResources.count > 20 {
+                fittingResources = fittingResources.lazy.sorted(by: { $0.date ?? .distantPast < $1.date ?? .distantPast }).suffix(10)
+                print("Reduced to the following 20 resources: \(fittingResources.map { $0.functionCallIdentifier }.joined(separator: ","))")
+            }
+
+            for resource in fittingResources {
                 print("Appending Resource: \(resource)")
+                let summary = try await resourceSummary.summarize(resource: resource)
+                print("Summary of Resource generated: \(summary)")
                 chat.append(
                     Chat(
                         role: .function,
-                        content: String(localized: "This is the content of the requested \(requestedResource):\n\n\(resource.jsonDescription)"),
+                        content: String(localized: "This is the summary of the requested \(requestedResource):\n\n\(summary.description)"),
                         name: LLMFunction.getResourcesName
                     )
                 )

diff --git a/LLMonFHIR/FHIR Interpretation/FHIRResource+Extensions.swift b/LLMonFHIR/FHIR Interpretation/FHIRResource+Extensions.swift
@@ -6,11 +6,20 @@
 // SPDX-License-Identifier: MIT
 //
 
+import Foundation
 import SpeziFHIR
 
 
 extension FHIRResource {
+    private static let dateFormatter: DateFormatter = {
+        let dateFormatter = DateFormatter()
+        dateFormatter.dateStyle = .short
+        return dateFormatter
+    }()
+
     var functionCallIdentifier: String {
-        resourceType.filter { !$0.isWhitespace } + displayName.filter { !$0.isWhitespace }
+        resourceType.filter { !$0.isWhitespace }
+            + displayName.filter { !$0.isWhitespace }
+            + (date.map { FHIRResource.dateFormatter.string(from: $0) } ?? "")
     }
 }
diff --git a/LLMonFHIR/FHIR Interpretation/FHIRStore+Extensions.swift b/LLMonFHIR/FHIR Interpretation/FHIRStore+Extensions.swift
@@ -8,6 +8,7 @@
 
 import ModelsR4
 import SpeziFHIR
+import SwiftUI
 
 
 extension FHIRStore {
@@ -16,7 +17,26 @@ extension FHIRStore {
     }
 
     var allResourcesFunctionCallIdentifier: [String] {
-        Array(Set(allResources.map { $0.functionCallIdentifier }))
+        @AppStorage(StorageKeys.resourceLimit) var resourceLimit = StorageKeys.Defaults.resourceLimit
+
+        let relevantResources: [FHIRResource]
+        if allResources.count > resourceLimit {
+            var limitedResources: [FHIRResource] = []
+            limitedResources.append(contentsOf: allergyIntolerances.dateSuffix(maxLength: resourceLimit / 9))
+            limitedResources.append(contentsOf: conditions.dateSuffix(maxLength: resourceLimit / 9))
+            limitedResources.append(contentsOf: diagnostics.dateSuffix(maxLength: resourceLimit / 9))
+            limitedResources.append(contentsOf: encounters.dateSuffix(maxLength: resourceLimit / 9))
+            limitedResources.append(contentsOf: immunizations.dateSuffix(maxLength: resourceLimit / 9))
+            limitedResources.append(contentsOf: medications.dateSuffix(maxLength: resourceLimit / 9))
+            limitedResources.append(contentsOf: observations.dateSuffix(maxLength: resourceLimit / 9))
+            limitedResources.append(contentsOf: otherResources.dateSuffix(maxLength: resourceLimit / 9))
+            limitedResources.append(contentsOf: procedures.dateSuffix(maxLength: resourceLimit / 9))
+            relevantResources = limitedResources
+        } else {
+            relevantResources = allResources
+        }
+
+        return Array(Set(relevantResources.map { $0.functionCallIdentifier }))
     }
 
 
@@ -38,3 +58,10 @@ extension FHIRStore {
         }
     }
 }
+
+
+extension Array where Element == FHIRResource {
+    fileprivate func dateSuffix(maxLength: Int) -> [FHIRResource] {
+        self.lazy.sorted(by: { $0.date ?? .distantPast < $1.date ?? .distantPast }).suffix(maxLength)
+    }
+}
diff --git a/LLMonFHIR/Resources/Localizable.xcstrings b/LLMonFHIR/Resources/Localizable.xcstrings
@@ -1206,7 +1206,7 @@
         "en" : {
           "stringUnit" : {
             "state" : "translated",
-            "value" : "You are the LLM on FHIR application.\nYour task is to interpret FHIR resources from the user's clinical records.\n\nThroughout the conversation with the user, use the \"get_resources\" function to obtain the FHIR health resources necessary to properly answer the users question. For example, if the user asks about their allergies, you must use the \"get_resources\" function to output the FHIR resource titles for allergy records so you can then use them to answer the question. The end goal is to answer the users question in the best way possible while taking the FHIR resources obtained using \"get_resources\" into consideration.\n\nThese are the resource titles of the resources you can request using \"get_resources\":\n{{FHIR_RESOURCE}}\n\nInterpret the resources by explaining its data relevant to the user's health.\nExplain the relevant medical context in a language understandable by a user who is not a medical professional, ideally in a 5th grade reading level.\nYou should provide factual and precise information in a compact summary in short responses.\n\nDo not introduce yourself at the beginning, and start with your interpretation. \n\nImmediately return a short summary of the users health records to start the conversation.\nThe initial summary should be a short and simple summary and NOT just list the titles of the records.\nEnd with a question asking user if they have any questions. Make sure that this question is not generic but specific to their health records.\nMake sure your response is in the same language the user writes to you in.\nThe tense should be present."
+            "value" : "You are the LLM on FHIR application.\nYour task is to interpret FHIR resources from the user's clinical records.\n\nThroughout the conversation with the user, use the \"get_resources\" function to obtain the FHIR health resources necessary to answer the user's question properly. For example, if the user asks about their allergies, you must use the \"get_resources\" function to output the FHIR resource titles for allergy records so you can then use them to answer the question. The end goal is to answer the user's question in the best way possible while taking the FHIR resources obtained using \"get_resources\" into consideration.\n\nIf there is a Patient FHIR resource available, ensure that you request this resource first to get adequate information about the patient. Only request relevant resources and focus on recent resources. Try to reduce the number of requested resources to a reasonable scope.\n\nThese are the resource titles of the resources you can request using \"get_resources\":\n{{FHIR_RESOURCE}}\n\nInterpret the resources by explaining the data relevant to the user's health.\nExplain the relevant medical context in a language understandable by a user who is not a medical professional, ideally at a 5th-grade reading level.\nYou should provide factual and precise information in a compact summary in short responses.\n\nDo not introduce yourself at the beginning, and start with your interpretation. \n\nImmediately return a summary of the user's health records to start the conversation.\nThe initial summary should be short and simple and NOT list the records' titles or any resource's detailed content; stay at a high level.\nEnd with a question asking the user if they have any questions. Make sure that this question is not generic but specific to their health records.\nMake sure your response is in the same language the user writes to you in.\nThe tense should be present."
           }
         }
       }
@@ -1373,6 +1373,26 @@
         }
       }
     },
+    "Resource Limit" : {
+      "localizations" : {
+        "en" : {
+          "stringUnit" : {
+            "state" : "translated",
+            "value" : "Resource Limit"
+          }
+        }
+      }
+    },
+    "Resource Limit %lld" : {
+      "localizations" : {
+        "en" : {
+          "stringUnit" : {
+            "state" : "translated",
+            "value" : "Resource Limit %lld"
+          }
+        }
+      }
+    },
     "Resource Selection" : {
       "localizations" : {
         "en" : {
@@ -1785,12 +1805,12 @@
         }
       }
     },
-    "This is the content of the requested %@:\n\n%@" : {
+    "This is the summary of the requested %@:\n\n%@" : {
       "localizations" : {
         "en" : {
           "stringUnit" : {
             "state" : "new",
-            "value" : "This is the content of the requested %1$@:\n\n%2$@"
+            "value" : "This is the summary of the requested %1$@:\n\n%2$@"
           }
         }
       }

diff --git a/...urces/Mock Patients/Beatris270_Bogan287_5b3645de-a2d0-d016-0839-bab3757c4c58.json.license b/...urces/Mock Patients/Beatris270_Bogan287_5b3645de-a2d0-d016-0839-bab3757c4c58.json.license
@@ -5,4 +5,4 @@ SPDX-FileCopyrightText: 2023 Stanford University
 
 SPDX-License-Identifier: MIT
 
-The patient mock data is generated by Synthea: https://github.com/synthetichealth/synthea: 
+The patient mock data is generated by Synthea: https://github.com/synthetichealth/synthea: Jason Walonoski, Mark Kramer, Joseph Nichols, Andre Quina, Chris Moesel, Dylan Hall, Carlton Duffett, Kudakwashe Dube, Thomas Gallagher, Scott McLachlan, Synthea: An approach, method, and software mechanism for generating synthetic patients and the synthetic electronic health care record, Journal of the American Medical Informatics Association, Volume 25, Issue 3, March 2018, Pages 230–238, https://doi.org/10.1093/jamia/ocx079
diff --git a/LLMonFHIR/Settings/SettingsView.swift b/LLMonFHIR/Settings/SettingsView.swift
@@ -32,6 +32,7 @@ struct SettingsView: View {
             List {
                 openAISettings
                 speechSettings
+                resourcesLimitSettings
                 resourcesSettings
                 promptsSettings
             }
@@ -57,6 +58,14 @@ struct SettingsView: View {
         }
     }
 
+    private var resourcesLimitSettings: some View {
+        Section("Resource Limit") {
+            Stepper(value: $resourceLimit, in: 10...2000, step: 10) {
+                Text("Resource Limit \(resourceLimit)")
+            }
+        }
+    }
+
     private var resourcesSettings: some View {
         Section("Resource Selection") {
             NavigationLink(value: SettingsDestinations.resourceSelection) {

diff --git a/LLMonFHIR/SharedContext/StorageKeys.swift b/LLMonFHIR/SharedContext/StorageKeys.swift
@@ -10,7 +10,7 @@
 enum StorageKeys {
     enum Defaults {
         static let enableTextToSpeech = false
-        static let resourceLimit = 50
+        static let resourceLimit = 250
     }
 
 

diff --git a/LLMonFHIRUITests/FHIRDisplayTests.swift b/LLMonFHIRUITests/FHIRDisplayTests.swift
@@ -25,7 +25,7 @@ final class FHIRDisplayTests: XCTestCase {
 
         app.swipeUp()
 
-        let mockResource = app.otherElements.buttons["Mock Resource"]
+        let mockResource = app.staticTexts["Mock Resource"]
         XCTAssertTrue(mockResource.exists, "The 'Mock Resource' does not exist.")
 
         mockResource.tap()
Original file line number	Diff line number	Diff line change
Expand Up		@@ -5,4 +5,4 @@ SPDX-FileCopyrightText: 2023 Stanford University

		SPDX-License-Identifier: MIT

		The patient mock data is generated by Synthea: https://github.com/synthetichealth/synthea:
		The patient mock data is generated by Synthea: https://github.com/synthetichealth/synthea: Jason Walonoski, Mark Kramer, Joseph Nichols, Andre Quina, Chris Moesel, Dylan Hall, Carlton Duffett, Kudakwashe Dube, Thomas Gallagher, Scott McLachlan, Synthea: An approach, method, and software mechanism for generating synthetic patients and the synthetic electronic health care record, Journal of the American Medical Informatics Association, Volume 25, Issue 3, March 2018, Pages 230–238, https://doi.org/10.1093/jamia/ocx079