From cdfeda1bfaf47a6bbf58c75b5b8660326e59389e Mon Sep 17 00:00:00 2001 From: Paul Schmiedmayer Date: Thu, 14 Dec 2023 18:52:34 -0800 Subject: [PATCH 1/6] Update Setup and Automate Tests --- LLMonFHIR.xcodeproj/project.pbxproj | 20 - .../xcshareddata/xcschemes/LLMonFHIR.xcscheme | 2 +- .../FHIRMultipleResourceInterpreter.swift | 19 +- .../FHIRResourceInterpreter+Extensions.swift | 29 - .../FHIRStore+Extensions.swift | 1 + LLMonFHIR/Mock Data/MockData.swift | 66 +- LLMonFHIR/Resources/Localizable.xcstrings | 5 +- ..._ff0e4d0e-6181-e36e-d817-64dbcaecb5d0.json | 25854 ---- ...e-6181-e36e-d817-64dbcaecb5d0.json.license | 8 - ..._b5fab35c-8cd1-49f0-b28c-122866af8614.json | 90439 ------------ ...c-8cd1-49f0-b28c-122866af8614.json.license | 8 - ..._10acd373-14d9-6077-f0fc-790e06d7c6c5.json | 31660 ----- ...3-14d9-6077-f0fc-790e06d7c6c5.json.license | 8 - ..._5b70be80-a0f2-849f-a286-8a8d2eab86b9.json | 108679 --------------- ...0-a0f2-849f-a286-8a8d2eab86b9.json.license | 8 - LLMonFHIR/Settings/ResourceSelection.swift | 8 +- LLMonFHIR/SharedContext/FeatureFlags.swift | 2 + LLMonFHIRUITests/FHIRDisplayTests.swift | 70 +- 18 files changed, 85 insertions(+), 256801 deletions(-) delete mode 100644 LLMonFHIR/FHIR Interpretation/FHIRResourceInterpreter+Extensions.swift delete mode 100644 LLMonFHIR/Resources/Mock Patients/Domingo513_Bashirian201_ff0e4d0e-6181-e36e-d817-64dbcaecb5d0.json delete mode 100644 LLMonFHIR/Resources/Mock Patients/Domingo513_Bashirian201_ff0e4d0e-6181-e36e-d817-64dbcaecb5d0.json.license delete mode 100644 LLMonFHIR/Resources/Mock Patients/Gregoria352_Shan714_Koss676_b5fab35c-8cd1-49f0-b28c-122866af8614.json delete mode 100644 LLMonFHIR/Resources/Mock Patients/Gregoria352_Shan714_Koss676_b5fab35c-8cd1-49f0-b28c-122866af8614.json.license delete mode 100644 LLMonFHIR/Resources/Mock Patients/Micah422_Stehr398_10acd373-14d9-6077-f0fc-790e06d7c6c5.json delete mode 100644 LLMonFHIR/Resources/Mock Patients/Micah422_Stehr398_10acd373-14d9-6077-f0fc-790e06d7c6c5.json.license delete mode 100644 LLMonFHIR/Resources/Mock Patients/Porfirio146_Jakubowski832_5b70be80-a0f2-849f-a286-8a8d2eab86b9.json delete mode 100644 LLMonFHIR/Resources/Mock Patients/Porfirio146_Jakubowski832_5b70be80-a0f2-849f-a286-8a8d2eab86b9.json.license diff --git a/LLMonFHIR.xcodeproj/project.pbxproj b/LLMonFHIR.xcodeproj/project.pbxproj index 9c26497..38c7bee 100644 --- a/LLMonFHIR.xcodeproj/project.pbxproj +++ b/LLMonFHIR.xcodeproj/project.pbxproj @@ -15,12 +15,9 @@ 2F036EA12B0E4B22009B2745 /* FHIRInterpretationModule.swift in Sources */ = {isa = PBXBuildFile; fileRef = 2F036EA02B0E4B22009B2745 /* FHIRInterpretationModule.swift */; }; 2F036EA32B0EC9BC009B2745 /* FHIRStore+Extensions.swift in Sources */ = {isa = PBXBuildFile; fileRef = 2F036EA22B0EC9BC009B2745 /* FHIRStore+Extensions.swift */; }; 2F036EA52B0ED1F0009B2745 /* FHIRResourcesInstructionsView.swift in Sources */ = {isa = PBXBuildFile; fileRef = 2F036EA42B0ED1F0009B2745 /* FHIRResourcesInstructionsView.swift */; }; - 2F036EB32B0EEAD6009B2745 /* Porfirio146_Jakubowski832_5b70be80-a0f2-849f-a286-8a8d2eab86b9.json in Resources */ = {isa = PBXBuildFile; fileRef = 2F036EA92B0EEAD5009B2745 /* Porfirio146_Jakubowski832_5b70be80-a0f2-849f-a286-8a8d2eab86b9.json */; }; 2F036EB42B0EEAD6009B2745 /* Jacklyn830_Veum823_e0e1f21a-22a7-d166-7bb1-63f6bbce1a32.json in Resources */ = {isa = PBXBuildFile; fileRef = 2F036EAA2B0EEAD5009B2745 /* Jacklyn830_Veum823_e0e1f21a-22a7-d166-7bb1-63f6bbce1a32.json */; }; 2F036EB52B0EEAD6009B2745 /* Gonzalo160_Duenas839_ed70a28f-30b2-acb7-658a-8b340dadd685.json in Resources */ = {isa = PBXBuildFile; fileRef = 2F036EAB2B0EEAD5009B2745 /* Gonzalo160_Duenas839_ed70a28f-30b2-acb7-658a-8b340dadd685.json */; }; - 2F036EB82B0EEAD6009B2745 /* Gregoria352_Shan714_Koss676_b5fab35c-8cd1-49f0-b28c-122866af8614.json in Resources */ = {isa = PBXBuildFile; fileRef = 2F036EAE2B0EEAD6009B2745 /* Gregoria352_Shan714_Koss676_b5fab35c-8cd1-49f0-b28c-122866af8614.json */; }; 2F036EB92B0EEAD6009B2745 /* Beatris270_Bogan287_5b3645de-a2d0-d016-0839-bab3757c4c58.json in Resources */ = {isa = PBXBuildFile; fileRef = 2F036EAF2B0EEAD6009B2745 /* Beatris270_Bogan287_5b3645de-a2d0-d016-0839-bab3757c4c58.json */; }; - 2F036EBB2B0EEAD6009B2745 /* Micah422_Stehr398_10acd373-14d9-6077-f0fc-790e06d7c6c5.json in Resources */ = {isa = PBXBuildFile; fileRef = 2F036EB12B0EEAD6009B2745 /* Micah422_Stehr398_10acd373-14d9-6077-f0fc-790e06d7c6c5.json */; }; 2F036EBF2B0EEB10009B2745 /* MockData.swift in Sources */ = {isa = PBXBuildFile; fileRef = 2F036EBE2B0EEB10009B2745 /* MockData.swift */; }; 2F036EC12B0EEE07009B2745 /* ResourceSelection.swift in Sources */ = {isa = PBXBuildFile; fileRef = 2F036EC02B0EEE07009B2745 /* ResourceSelection.swift */; }; 2F0F90BA2A1E6556006D7E03 /* SettingsView.swift in Sources */ = {isa = PBXBuildFile; fileRef = 2F0F90B92A1E6556006D7E03 /* SettingsView.swift */; }; @@ -28,7 +25,6 @@ 2F49B7762980407C00BCB272 /* Spezi in Frameworks */ = {isa = PBXBuildFile; productRef = 2F49B7752980407B00BCB272 /* Spezi */; }; 2F4E237E2989A2FE0013F3D9 /* OnboardingTests.swift in Sources */ = {isa = PBXBuildFile; fileRef = 2F4E237D2989A2FE0013F3D9 /* OnboardingTests.swift */; }; 2F4E23832989D51F0013F3D9 /* LLMonFHIRTestingSetup.swift in Sources */ = {isa = PBXBuildFile; fileRef = 2F4E23822989D51F0013F3D9 /* LLMonFHIRTestingSetup.swift */; }; - 2F55FC532A1AE8750051DF48 /* FHIRResourceInterpreter+Extensions.swift in Sources */ = {isa = PBXBuildFile; fileRef = 2F55FC522A1AE8750051DF48 /* FHIRResourceInterpreter+Extensions.swift */; }; 2F5BD9D12A78AAED0004E0AC /* String+LocalizedError.swift in Sources */ = {isa = PBXBuildFile; fileRef = 2F5BD9D02A78AAED0004E0AC /* String+LocalizedError.swift */; }; 2F5E32BD297E05EA003432F8 /* LLMonFHIRDelegate.swift in Sources */ = {isa = PBXBuildFile; fileRef = 2F5E32BC297E05EA003432F8 /* LLMonFHIRDelegate.swift */; }; 2F901CE22A1A03360007C167 /* SpeziOpenAI in Frameworks */ = {isa = PBXBuildFile; productRef = 2F901CE12A1A03360007C167 /* SpeziOpenAI */; }; @@ -40,7 +36,6 @@ 2FD024902B1171EC009A682C /* Pasquale620_Kuhn96_792a51c0-a2a4-ee26-c23c-7cb24f8a0e35.json in Resources */ = {isa = PBXBuildFile; fileRef = 2FD0248C2B1171EC009A682C /* Pasquale620_Kuhn96_792a51c0-a2a4-ee26-c23c-7cb24f8a0e35.json */; }; 2FD024912B1171EC009A682C /* Edythe31_Morar593_9c3df38a-d3b7-2198-3898-51f9153d023d.json in Resources */ = {isa = PBXBuildFile; fileRef = 2FD0248D2B1171EC009A682C /* Edythe31_Morar593_9c3df38a-d3b7-2198-3898-51f9153d023d.json */; }; 2FD024922B1171EC009A682C /* Milton509_Ortiz186_d66b5418-06cb-fc8a-8c13-85685b6ac939.json in Resources */ = {isa = PBXBuildFile; fileRef = 2FD0248E2B1171EC009A682C /* Milton509_Ortiz186_d66b5418-06cb-fc8a-8c13-85685b6ac939.json */; }; - 2FD024932B1171EC009A682C /* Domingo513_Bashirian201_ff0e4d0e-6181-e36e-d817-64dbcaecb5d0.json in Resources */ = {isa = PBXBuildFile; fileRef = 2FD0248F2B1171EC009A682C /* Domingo513_Bashirian201_ff0e4d0e-6181-e36e-d817-64dbcaecb5d0.json */; }; 2FD8E8272A1AAD9B00357F4E /* LLMonFHIRStandard.swift in Sources */ = {isa = PBXBuildFile; fileRef = 2FD8E8262A1AAD9B00357F4E /* LLMonFHIRStandard.swift */; }; 2FD8E82A2A1AADDA00357F4E /* ModelsDSTU2 in Frameworks */ = {isa = PBXBuildFile; productRef = 2FD8E8292A1AADDA00357F4E /* ModelsDSTU2 */; }; 2FD8E82C2A1AADDA00357F4E /* ModelsR4 in Frameworks */ = {isa = PBXBuildFile; productRef = 2FD8E82B2A1AADDA00357F4E /* ModelsR4 */; }; @@ -91,19 +86,15 @@ 2F036EA02B0E4B22009B2745 /* FHIRInterpretationModule.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = FHIRInterpretationModule.swift; sourceTree = ""; }; 2F036EA22B0EC9BC009B2745 /* FHIRStore+Extensions.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; 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sourceTree = ""; }; - 2F036EAE2B0EEAD6009B2745 /* Gregoria352_Shan714_Koss676_b5fab35c-8cd1-49f0-b28c-122866af8614.json */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text.json; path = "Gregoria352_Shan714_Koss676_b5fab35c-8cd1-49f0-b28c-122866af8614.json"; sourceTree = ""; }; 2F036EAF2B0EEAD6009B2745 /* Beatris270_Bogan287_5b3645de-a2d0-d016-0839-bab3757c4c58.json */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text.json; path = "Beatris270_Bogan287_5b3645de-a2d0-d016-0839-bab3757c4c58.json"; sourceTree = ""; }; - 2F036EB12B0EEAD6009B2745 /* Micah422_Stehr398_10acd373-14d9-6077-f0fc-790e06d7c6c5.json */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text.json; path = "Micah422_Stehr398_10acd373-14d9-6077-f0fc-790e06d7c6c5.json"; sourceTree = ""; }; 2F036EBE2B0EEB10009B2745 /* MockData.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = MockData.swift; sourceTree = ""; }; 2F036EC02B0EEE07009B2745 /* ResourceSelection.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = ResourceSelection.swift; sourceTree = ""; }; 2F0F90B92A1E6556006D7E03 /* SettingsView.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = SettingsView.swift; sourceTree = ""; }; 2F42429A2A8B14AC006E2B01 /* OpenAIAPIKey.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = OpenAIAPIKey.swift; sourceTree = ""; }; 2F4E237D2989A2FE0013F3D9 /* OnboardingTests.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = OnboardingTests.swift; sourceTree = ""; }; 2F4E23822989D51F0013F3D9 /* LLMonFHIRTestingSetup.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = LLMonFHIRTestingSetup.swift; sourceTree = ""; }; - 2F55FC522A1AE8750051DF48 /* FHIRResourceInterpreter+Extensions.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = "FHIRResourceInterpreter+Extensions.swift"; sourceTree = ""; }; 2F5BD9D02A78AAED0004E0AC /* String+LocalizedError.swift */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.swift; path = "String+LocalizedError.swift"; sourceTree = ""; }; 2F5E32BC297E05EA003432F8 /* LLMonFHIRDelegate.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = LLMonFHIRDelegate.swift; sourceTree = ""; }; 2FAEC07F297F583900C11C42 /* LLMonFHIR.entitlements */ = {isa = PBXFileReference; lastKnownFileType = text.plist.entitlements; path = LLMonFHIR.entitlements; sourceTree = ""; }; @@ -115,7 +106,6 @@ 2FD0248C2B1171EC009A682C /* Pasquale620_Kuhn96_792a51c0-a2a4-ee26-c23c-7cb24f8a0e35.json */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text.json; path = "Pasquale620_Kuhn96_792a51c0-a2a4-ee26-c23c-7cb24f8a0e35.json"; sourceTree = ""; }; 2FD0248D2B1171EC009A682C /* Edythe31_Morar593_9c3df38a-d3b7-2198-3898-51f9153d023d.json */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text.json; path = "Edythe31_Morar593_9c3df38a-d3b7-2198-3898-51f9153d023d.json"; sourceTree = ""; }; 2FD0248E2B1171EC009A682C /* Milton509_Ortiz186_d66b5418-06cb-fc8a-8c13-85685b6ac939.json */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text.json; path = "Milton509_Ortiz186_d66b5418-06cb-fc8a-8c13-85685b6ac939.json"; sourceTree = ""; }; - 2FD0248F2B1171EC009A682C /* Domingo513_Bashirian201_ff0e4d0e-6181-e36e-d817-64dbcaecb5d0.json */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text.json; path = "Domingo513_Bashirian201_ff0e4d0e-6181-e36e-d817-64dbcaecb5d0.json"; sourceTree = ""; }; 2FD8E8262A1AAD9B00357F4E /* LLMonFHIRStandard.swift */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.swift; path = LLMonFHIRStandard.swift; sourceTree = ""; }; 2FD8E8322A1AB68E00357F4E /* FHIRResource+Extensions.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = "FHIRResource+Extensions.swift"; sourceTree = ""; }; 2FD8E83A2A1AD10300357F4E /* FHIRResourcesView.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = FHIRResourcesView.swift; sourceTree = ""; }; @@ -185,15 +175,11 @@ isa = PBXGroup; children = ( 2F036EAF2B0EEAD6009B2745 /* Beatris270_Bogan287_5b3645de-a2d0-d016-0839-bab3757c4c58.json */, - 2FD0248F2B1171EC009A682C /* Domingo513_Bashirian201_ff0e4d0e-6181-e36e-d817-64dbcaecb5d0.json */, 2FD0248D2B1171EC009A682C /* Edythe31_Morar593_9c3df38a-d3b7-2198-3898-51f9153d023d.json */, 2F036EAB2B0EEAD5009B2745 /* Gonzalo160_Duenas839_ed70a28f-30b2-acb7-658a-8b340dadd685.json */, - 2F036EAE2B0EEAD6009B2745 /* Gregoria352_Shan714_Koss676_b5fab35c-8cd1-49f0-b28c-122866af8614.json */, 2F036EAA2B0EEAD5009B2745 /* Jacklyn830_Veum823_e0e1f21a-22a7-d166-7bb1-63f6bbce1a32.json */, - 2F036EB12B0EEAD6009B2745 /* Micah422_Stehr398_10acd373-14d9-6077-f0fc-790e06d7c6c5.json */, 2FD0248E2B1171EC009A682C /* Milton509_Ortiz186_d66b5418-06cb-fc8a-8c13-85685b6ac939.json */, 2FD0248C2B1171EC009A682C /* Pasquale620_Kuhn96_792a51c0-a2a4-ee26-c23c-7cb24f8a0e35.json */, - 2F036EA92B0EEAD5009B2745 /* Porfirio146_Jakubowski832_5b70be80-a0f2-849f-a286-8a8d2eab86b9.json */, ); path = "Mock Patients"; sourceTree = ""; @@ -234,7 +220,6 @@ 433352432A5C96090043A440 /* FHIRMultipleResourceInterpreter.swift */, 2FD024882B116EEF009A682C /* LLMFunction.swift */, 2FD0248A2B116EF6009A682C /* LLMStreamResult.swift */, - 2F55FC522A1AE8750051DF48 /* FHIRResourceInterpreter+Extensions.swift */, ); path = "FHIR Interpretation"; sourceTree = ""; @@ -504,13 +489,9 @@ 2FD024912B1171EC009A682C /* Edythe31_Morar593_9c3df38a-d3b7-2198-3898-51f9153d023d.json in Resources */, 2F036EB42B0EEAD6009B2745 /* Jacklyn830_Veum823_e0e1f21a-22a7-d166-7bb1-63f6bbce1a32.json in Resources */, 2F036EB52B0EEAD6009B2745 /* Gonzalo160_Duenas839_ed70a28f-30b2-acb7-658a-8b340dadd685.json in Resources */, - 2F036EB82B0EEAD6009B2745 /* Gregoria352_Shan714_Koss676_b5fab35c-8cd1-49f0-b28c-122866af8614.json in Resources */, 2FD024922B1171EC009A682C /* Milton509_Ortiz186_d66b5418-06cb-fc8a-8c13-85685b6ac939.json in Resources */, 2FC186092AD52FFF0065EBB2 /* Localizable.xcstrings in Resources */, 2F036EB92B0EEAD6009B2745 /* Beatris270_Bogan287_5b3645de-a2d0-d016-0839-bab3757c4c58.json in Resources */, - 2F036EB32B0EEAD6009B2745 /* Porfirio146_Jakubowski832_5b70be80-a0f2-849f-a286-8a8d2eab86b9.json in Resources */, - 2F036EBB2B0EEAD6009B2745 /* Micah422_Stehr398_10acd373-14d9-6077-f0fc-790e06d7c6c5.json in Resources */, - 2FD024932B1171EC009A682C /* Domingo513_Bashirian201_ff0e4d0e-6181-e36e-d817-64dbcaecb5d0.json in Resources */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -581,7 +562,6 @@ 2FD8E8272A1AAD9B00357F4E /* LLMonFHIRStandard.swift in Sources */, 2FD0248B2B116EF6009A682C /* LLMStreamResult.swift in Sources */, 2F5E32BD297E05EA003432F8 /* LLMonFHIRDelegate.swift in Sources */, - 2F55FC532A1AE8750051DF48 /* FHIRResourceInterpreter+Extensions.swift in Sources */, 653A2551283387FE005D4D48 /* LLMonFHIR.swift in Sources */, 2F036EA52B0ED1F0009B2745 /* FHIRResourcesInstructionsView.swift in Sources */, 2FE5DC3629EDD7CA004B9AB4 /* HealthKitPermissions.swift in Sources */, diff --git a/LLMonFHIR.xcodeproj/xcshareddata/xcschemes/LLMonFHIR.xcscheme b/LLMonFHIR.xcodeproj/xcshareddata/xcschemes/LLMonFHIR.xcscheme index e6593ac..7d9539b 100644 --- a/LLMonFHIR.xcodeproj/xcshareddata/xcschemes/LLMonFHIR.xcscheme +++ b/LLMonFHIR.xcodeproj/xcshareddata/xcschemes/LLMonFHIR.xcscheme @@ -23,7 +23,7 @@ diff --git a/LLMonFHIR/FHIR Interpretation/FHIRMultipleResourceInterpreter.swift b/LLMonFHIR/FHIR Interpretation/FHIRMultipleResourceInterpreter.swift index cc7dbba..d789950 100644 --- a/LLMonFHIR/FHIR Interpretation/FHIRMultipleResourceInterpreter.swift +++ b/LLMonFHIR/FHIR Interpretation/FHIRMultipleResourceInterpreter.swift @@ -79,26 +79,19 @@ class FHIRMultipleResourceInterpreter { } private func prepareSystemPrompt() { + var prompt = FHIRPrompt.interpretMultipleResources.prompt + if let patient = fhirStore.patient { + prompt.append(patient.jsonDescription) + } + if chat.isEmpty { chat = [ Chat( role: .system, - content: FHIRPrompt.interpretMultipleResources.prompt + content: prompt ) ] } - - if let patient = fhirStore.patient { - chat.append( - Chat( - role: .system, - content: String( - localized: "Here is the JSON content of the patient resource as an initial context: \n\n \(patient.jsonDescription)", - comment: "System prompt used by the FHIRMultipleResourceInterpreter to pass in the patient JSON." - ) - ) - ) - } } private func executeLLMQueries() async throws { diff --git a/LLMonFHIR/FHIR Interpretation/FHIRResourceInterpreter+Extensions.swift b/LLMonFHIR/FHIR Interpretation/FHIRResourceInterpreter+Extensions.swift deleted file mode 100644 index 6470d54..0000000 --- a/LLMonFHIR/FHIR Interpretation/FHIRResourceInterpreter+Extensions.swift +++ /dev/null @@ -1,29 +0,0 @@ -// -// This source file is part of the Stanford LLM on FHIR project -// -// SPDX-FileCopyrightText: 2023 Stanford University -// -// SPDX-License-Identifier: MIT -// - -import SpeziFHIR -import SpeziFHIRInterpretation -import SpeziOpenAI - - -extension FHIRResourceInterpreter { - func chat(forResource resource: FHIRResource) -> [Chat] { - var chat = [ - Chat( - role: .system, - content: FHIRPrompt.interpretation.prompt(withFHIRResource: resource.jsonDescription) - ) - ] - - if let interpretation = cachedInterpretation(forResource: resource) { - chat.append(Chat(role: .assistant, content: interpretation)) - } - - return chat - } -} diff --git a/LLMonFHIR/FHIR Interpretation/FHIRStore+Extensions.swift b/LLMonFHIR/FHIR Interpretation/FHIRStore+Extensions.swift index 0b0f850..d00325b 100644 --- a/LLMonFHIR/FHIR Interpretation/FHIRStore+Extensions.swift +++ b/LLMonFHIR/FHIR Interpretation/FHIRStore+Extensions.swift @@ -131,6 +131,7 @@ extension FHIRStore { if FeatureFlags.testMode { let mockObservation = Observation( code: CodeableConcept(coding: [Coding(code: "1234".asFHIRStringPrimitive())]), + id: FHIRPrimitive("1234"), issued: FHIRPrimitive(try? Instant(date: .now)), status: FHIRPrimitive(ObservationStatus.final) ) diff --git a/LLMonFHIR/Mock Data/MockData.swift b/LLMonFHIR/Mock Data/MockData.swift index b76c20f..e193a7d 100644 --- a/LLMonFHIR/Mock Data/MockData.swift +++ b/LLMonFHIR/Mock Data/MockData.swift @@ -27,21 +27,6 @@ extension ModelsR4.Bundle { } } - private static var _domingo513Bashirian201: ModelsR4.Bundle? - static var domingo513Bashirian201: ModelsR4.Bundle { - get async { - if let domingo513Bashirian201 = _domingo513Bashirian201 { - return domingo513Bashirian201 - } - - let domingo513Bashirian201 = await Foundation.Bundle.main.loadFHIRBundle( - withName: "Domingo513_Bashirian201_ff0e4d0e-6181-e36e-d817-64dbcaecb5d0" - ) - ModelsR4.Bundle._domingo513Bashirian201 = domingo513Bashirian201 - return domingo513Bashirian201 - } - } - private static var _edythe31Morar593: ModelsR4.Bundle? static var edythe31Morar593: ModelsR4.Bundle { get async { @@ -72,21 +57,6 @@ extension ModelsR4.Bundle { } } - private static var _gregoria352Shan714: ModelsR4.Bundle? - static var gregoria352Shan714: ModelsR4.Bundle { - get async { - if let gregoria352Shan714 = _gregoria352Shan714 { - return gregoria352Shan714 - } - - let gregoria352Shan714 = await Foundation.Bundle.main.loadFHIRBundle( - withName: "Gregoria352_Shan714_Koss676_b5fab35c-8cd1-49f0-b28c-122866af8614" - ) - ModelsR4.Bundle._gregoria352Shan714 = gregoria352Shan714 - return gregoria352Shan714 - } - } - private static var _jacklyn830Veum823: ModelsR4.Bundle? static var jacklyn830Veum823: ModelsR4.Bundle { get async { @@ -102,21 +72,6 @@ extension ModelsR4.Bundle { } } - private static var _micah422Stehr398: ModelsR4.Bundle? - static var micah422Stehr398: ModelsR4.Bundle { - get async { - if let micah422Stehr398 = _micah422Stehr398 { - return micah422Stehr398 - } - - let micah422Stehr398 = await Foundation.Bundle.main.loadFHIRBundle( - withName: "Micah422_Stehr398_10acd373-14d9-6077-f0fc-790e06d7c6c5" - ) - ModelsR4.Bundle._micah422Stehr398 = micah422Stehr398 - return micah422Stehr398 - } - } - private static var _milton509Ortiz186: ModelsR4.Bundle? static var milton509Ortiz186: ModelsR4.Bundle { get async { @@ -147,35 +102,16 @@ extension ModelsR4.Bundle { } } - private static var _porfirio146Jakubowski832: ModelsR4.Bundle? - static var porfirio146Jakubowski832: ModelsR4.Bundle { - get async { - if let porfirio146Jakubowski832 = _porfirio146Jakubowski832 { - return porfirio146Jakubowski832 - } - - let porfirio146Jakubowski832 = await Foundation.Bundle.main.loadFHIRBundle( - withName: "Porfirio146_Jakubowski832_5b70be80-a0f2-849f-a286-8a8d2eab86b9" - ) - ModelsR4.Bundle._porfirio146Jakubowski832 = porfirio146Jakubowski832 - return porfirio146Jakubowski832 - } - } - static var llmOnFHIRMockPatients: [Bundle] { get async { await [ .beatris270Bogan287, - .domingo513Bashirian201, .edythe31Morar593, .gonzalo160Duenas839, - .gregoria352Shan714, .jacklyn830Veum823, - .micah422Stehr398, .milton509Ortiz186, - .pasquale620Kuhn96, - .porfirio146Jakubowski832 + .pasquale620Kuhn96 ] } } diff --git a/LLMonFHIR/Resources/Localizable.xcstrings b/LLMonFHIR/Resources/Localizable.xcstrings index 9fdbedb..c71563d 100644 --- a/LLMonFHIR/Resources/Localizable.xcstrings +++ b/LLMonFHIR/Resources/Localizable.xcstrings @@ -1168,9 +1168,6 @@ } } }, - "Here is the JSON content of the patient resource as an initial context: \n\n %@" : { - "comment" : "System prompt used by the FHIRMultipleResourceInterpreter to pass in the patient JSON." - }, "Immunizations" : { "localizations" : { "en" : { @@ -1198,7 +1195,7 @@ "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 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\nE.g. if the user asks about their Medication it would be recommended to request all MedicationRequest FHIR resource types.\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 based on the FHIR patient resources if available to start the conversation. You may already request FHIR resources using the \"get_resources\" function.\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.\n" + "value" : "You are the LLM on FHIR application. Your 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. Leave out any technical details like JSON, FHIR resources, and other implementation details of the underlying data resources.\nOnly request relevant resources and focus on recent resources. Try to reduce the number of requested resources to a reasonable scope.\nE.g. if the user asks about their Medication it would be recommended to request all MedicationRequest FHIR resource types.\n\nInterpret the resources by explaining the data relevant to the user's health. Explain the relevant medical context in a language understandable by a user who is not a medical professional, ideally at a 5th-grade reading level. You 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 based on the FHIR patient resources if available to start the conversation. You may already request FHIR resources using the \"get_resources\" function. The initial summary should be short and simple and NOT list the records' titles or any resource's detailed content; stay at a high level. End 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. Make sure your response is in the same language the user writes to you in. The tense should be present.\n\nThe patient resource is provided as the initial context. Ensure to leave out any like SSN, passport number, and telephone number." } } } diff --git a/LLMonFHIR/Resources/Mock Patients/Domingo513_Bashirian201_ff0e4d0e-6181-e36e-d817-64dbcaecb5d0.json b/LLMonFHIR/Resources/Mock Patients/Domingo513_Bashirian201_ff0e4d0e-6181-e36e-d817-64dbcaecb5d0.json deleted file mode 100644 index fed5df2..0000000 --- a/LLMonFHIR/Resources/Mock Patients/Domingo513_Bashirian201_ff0e4d0e-6181-e36e-d817-64dbcaecb5d0.json +++ /dev/null @@ -1,25854 +0,0 @@ -{ - "resourceType": "Bundle", - "type": "transaction", - "entry": [ { - "fullUrl": "urn:uuid:ff0e4d0e-6181-e36e-d817-64dbcaecb5d0", - "resource": { - "resourceType": "Patient", - "id": "ff0e4d0e-6181-e36e-d817-64dbcaecb5d0", - "meta": { - "profile": [ "http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient" ] - }, - "text": { - "status": "generated", - "div": "
Generated by Synthea.Version identifier: master-branch-latest-7-gcc27279b\n . Person seed: -5830253423258833266 Population seed: 0
" - }, - "extension": [ { - "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race", - "extension": [ { - "url": "ombCategory", - "valueCoding": { - "system": "urn:oid:2.16.840.1.113883.6.238", - "code": "2106-3", - "display": "White" - } - }, { - "url": "text", - "valueString": "White" - } ] - }, { - "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity", - "extension": [ { - "url": "ombCategory", - "valueCoding": { - "system": "urn:oid:2.16.840.1.113883.6.238", - "code": "2186-5", - "display": "Not Hispanic or Latino" - } - }, { - "url": "text", - "valueString": "Not Hispanic or Latino" - } ] - }, { - "url": "http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName", - "valueString": "Ethel888 Hintz995" - }, { - "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex", - "valueCode": "M" - }, { - "url": "http://hl7.org/fhir/StructureDefinition/patient-birthPlace", - "valueAddress": { - "city": "Ware", - "state": "Massachusetts", - "country": "US" - } - }, { - "url": "http://synthetichealth.github.io/synthea/disability-adjusted-life-years", - "valueDecimal": 0.35302835836655333 - }, { - "url": "http://synthetichealth.github.io/synthea/quality-adjusted-life-years", - "valueDecimal": 12.646971641633447 - } ], - "identifier": [ { - "system": "https://github.com/synthetichealth/synthea", - "value": "ff0e4d0e-6181-e36e-d817-64dbcaecb5d0" - }, { - "type": { - "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/v2-0203", - "code": "MR", - "display": "Medical Record Number" - } ], - "text": "Medical Record Number" - }, - "system": "http://hospital.smarthealthit.org", - "value": "ff0e4d0e-6181-e36e-d817-64dbcaecb5d0" - }, { - "type": { - "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/v2-0203", - "code": "SS", - "display": "Social Security Number" - } ], - "text": "Social Security Number" - }, - "system": "http://hl7.org/fhir/sid/us-ssn", - "value": "999-12-9188" - } ], - "name": [ { - "use": "official", - "family": "Bashirian201", - "given": [ "Domingo513" ] - } ], - "telecom": [ { - "system": "phone", - "value": "555-202-6553", - "use": "home" - } ], - "gender": "male", - "birthDate": "1994-08-12", - "deceasedDateTime": "2008-04-04T08:43:40-04:00", - "address": [ { - "extension": [ { - "url": "http://hl7.org/fhir/StructureDefinition/geolocation", - "extension": [ { - "url": "latitude", - "valueDecimal": 41.65001048751461 - }, { - "url": "longitude", - "valueDecimal": -70.30715501505665 - } ] - } ], - "line": [ "799 Labadie Orchard Apt 88" ], - "city": "Barnstable", - "state": "MA", - "postalCode": "02655", - "country": "US" - } ], - "maritalStatus": { - "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/v3-MaritalStatus", - "code": "S", - "display": "Never Married" - } ], - "text": "Never Married" - }, - "multipleBirthBoolean": false, - "communication": [ { - "language": { - "coding": [ { - "system": "urn:ietf:bcp:47", - "code": "en-US", - "display": "English" - } ], - "text": "English" - } - } ] - }, - "request": { - "method": "POST", - "url": "Patient" - } - }, { - "fullUrl": "urn:uuid:edcfb1d5-397a-c006-6f54-5ecd8824d00f", - "resource": { - "resourceType": "Encounter", - "id": "edcfb1d5-397a-c006-6f54-5ecd8824d00f", - "meta": { - "profile": [ "http://hl7.org/fhir/us/core/StructureDefinition/us-core-encounter" ] - }, - "identifier": [ { - "use": "official", - "system": "https://github.com/synthetichealth/synthea", - "value": "edcfb1d5-397a-c006-6f54-5ecd8824d00f" - } ], - "status": "finished", - "class": { - "system": "http://terminology.hl7.org/CodeSystem/v3-ActCode", - "code": "AMB" - }, - "type": [ { - "coding": [ { - "system": "http://snomed.info/sct", - "code": "410620009", - "display": "Well child visit (procedure)" - } ], - "text": "Well child visit (procedure)" - } ], - "subject": { - "reference": "urn:uuid:ff0e4d0e-6181-e36e-d817-64dbcaecb5d0", - "display": "Domingo513 Bashirian201" - }, - "participant": [ { - "type": [ { - "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/v3-ParticipationType", - "code": "PPRF", - "display": "primary performer" - } ], - "text": "primary performer" - } ], - "period": { - "start": "1997-01-17T07:43:40-05:00", - "end": "1997-01-17T07:58:40-05:00" - }, - "individual": { - "reference": "Practitioner?identifier=http://hl7.org/fhir/sid/us-npi|9999983139", - "display": "Dr. Jayme42 Ryan260" - } - } ], - "period": { - "start": "1997-01-17T07:43:40-05:00", - "end": "1997-01-17T07:58:40-05:00" - }, - "location": [ { - "location": { - "reference": "Location?identifier=https://github.com/synthetichealth/synthea|5b33150a-edcb-3bed-b460-fb1f14f9e897", - "display": "PCP26041" - } - } ], - "serviceProvider": { - "reference": "Organization?identifier=https://github.com/synthetichealth/synthea|aac92e78-fb05-349b-ab75-da8d6048352f", - "display": "PCP26041" - } - }, - "request": { - "method": "POST", - "url": "Encounter" - } - }, { - "fullUrl": "urn:uuid:bf3ad326-81c9-8b30-846b-a82578c0f1de", - "resource": { - "resourceType": "Condition", - "id": "bf3ad326-81c9-8b30-846b-a82578c0f1de", - "meta": { - "profile": [ "http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition" ] - }, - "clinicalStatus": { - "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/condition-clinical", - "code": "active" - } ] - }, - "verificationStatus": { - "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/condition-ver-status", - "code": "confirmed" - } ] - }, - "category": [ { - "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/condition-category", - "code": "encounter-diagnosis", - "display": "Encounter Diagnosis" - } ] - } ], - "code": { - "coding": [ { - "system": "http://snomed.info/sct", - "code": "53741008", - "display": "Coronary Heart Disease" - } ], - "text": "Coronary Heart Disease" - }, - "subject": { - "reference": "urn:uuid:ff0e4d0e-6181-e36e-d817-64dbcaecb5d0" - }, - "encounter": { - "reference": "urn:uuid:edcfb1d5-397a-c006-6f54-5ecd8824d00f" - }, - "onsetDateTime": "1997-01-17T07:43:40-05:00", - "recordedDate": "1997-01-17T07:43:40-05:00" - }, - "request": { - "method": "POST", - "url": "Condition" - } - }, { - "fullUrl": "urn:uuid:7658a636-6452-2762-e432-ff4f5ad37642", - "resource": { - "resourceType": "MedicationRequest", - "id": "7658a636-6452-2762-e432-ff4f5ad37642", - "meta": { - "profile": [ "http://hl7.org/fhir/us/core/StructureDefinition/us-core-medicationrequest" ] - }, - "status": "stopped", - "intent": "order", - "medicationCodeableConcept": { - "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "312961", - "display": "Simvastatin 20 MG Oral Tablet" - } ], - "text": "Simvastatin 20 MG Oral Tablet" - }, - "subject": { - "reference": "urn:uuid:ff0e4d0e-6181-e36e-d817-64dbcaecb5d0" - }, - "encounter": { - "reference": "urn:uuid:edcfb1d5-397a-c006-6f54-5ecd8824d00f" - }, - "authoredOn": "1997-01-17T07:43:40-05:00", - "requester": { - "reference": "Practitioner?identifier=http://hl7.org/fhir/sid/us-npi|9999983139", - "display": "Dr. Jayme42 Ryan260" - } - }, - "request": { - "method": "POST", - 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"focal": true, - "coverage": { - "display": "Aetna" - } - } ], - "item": [ { - "sequence": 1, - "productOrService": { - "coding": [ { - "system": "http://snomed.info/sct", - "code": "410620009", - "display": "Well child visit (procedure)" - } ], - "text": "Well child visit (procedure)" - }, - "encounter": [ { - "reference": "urn:uuid:edcfb1d5-397a-c006-6f54-5ecd8824d00f" - } ] - } ], - "total": { - "value": 13.92, - "currency": "USD" - } - }, - "request": { - "method": "POST", - "url": "Claim" - } - }, { - "fullUrl": "urn:uuid:96904284-6c11-a127-bed8-a3d7860d2f9a", - "resource": { - "resourceType": "MedicationRequest", - "id": "96904284-6c11-a127-bed8-a3d7860d2f9a", - "meta": { - "profile": [ "http://hl7.org/fhir/us/core/StructureDefinition/us-core-medicationrequest" ] - }, - "status": "stopped", - "intent": "order", - "medicationCodeableConcept": { - "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "197361", - "display": "Amlodipine 5 MG Oral Tablet" - 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-This source file is part of the Stanford LLM on FHIR project - -SPDX-FileCopyrightText: 2023 Stanford University - -SPDX-License-Identifier: MIT - -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/Resources/Mock Patients/Gregoria352_Shan714_Koss676_b5fab35c-8cd1-49f0-b28c-122866af8614.json b/LLMonFHIR/Resources/Mock Patients/Gregoria352_Shan714_Koss676_b5fab35c-8cd1-49f0-b28c-122866af8614.json deleted file mode 100644 index 10855af..0000000 --- a/LLMonFHIR/Resources/Mock Patients/Gregoria352_Shan714_Koss676_b5fab35c-8cd1-49f0-b28c-122866af8614.json +++ /dev/null @@ -1,90439 +0,0 @@ -{ - 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} - } ] -} diff --git a/LLMonFHIR/Resources/Mock Patients/Gregoria352_Shan714_Koss676_b5fab35c-8cd1-49f0-b28c-122866af8614.json.license b/LLMonFHIR/Resources/Mock Patients/Gregoria352_Shan714_Koss676_b5fab35c-8cd1-49f0-b28c-122866af8614.json.license deleted file mode 100644 index 750aeae..0000000 --- a/LLMonFHIR/Resources/Mock Patients/Gregoria352_Shan714_Koss676_b5fab35c-8cd1-49f0-b28c-122866af8614.json.license +++ /dev/null @@ -1,8 +0,0 @@ - -This source file is part of the Stanford LLM on FHIR project - -SPDX-FileCopyrightText: 2023 Stanford University - -SPDX-License-Identifier: MIT - -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/Resources/Mock Patients/Micah422_Stehr398_10acd373-14d9-6077-f0fc-790e06d7c6c5.json b/LLMonFHIR/Resources/Mock Patients/Micah422_Stehr398_10acd373-14d9-6077-f0fc-790e06d7c6c5.json deleted file mode 100644 index 3cfebc9..0000000 --- a/LLMonFHIR/Resources/Mock Patients/Micah422_Stehr398_10acd373-14d9-6077-f0fc-790e06d7c6c5.json +++ /dev/null @@ -1,31660 +0,0 @@ -{ - 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-This source file is part of the Stanford LLM on FHIR project - -SPDX-FileCopyrightText: 2023 Stanford University - -SPDX-License-Identifier: MIT - -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/Resources/Mock Patients/Porfirio146_Jakubowski832_5b70be80-a0f2-849f-a286-8a8d2eab86b9.json b/LLMonFHIR/Resources/Mock Patients/Porfirio146_Jakubowski832_5b70be80-a0f2-849f-a286-8a8d2eab86b9.json deleted file mode 100644 index 28a9973..0000000 --- a/LLMonFHIR/Resources/Mock Patients/Porfirio146_Jakubowski832_5b70be80-a0f2-849f-a286-8a8d2eab86b9.json +++ /dev/null @@ -1,108679 +0,0 @@ -{ - 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"display": "CHILD & FAMILY SERVICES, INC." - } - }, { - "type": { - "coding": [ { - "system": "http://hl7.org/fhir/us/core/CodeSystem/us-core-provenance-participant-type", - "code": "transmitter", - "display": "Transmitter" - } ], - "text": "Transmitter" - }, - "who": { - "reference": "Practitioner?identifier=http://hl7.org/fhir/sid/us-npi|9999967794", - "display": "Dr. Taylor21 Haley279" - }, - "onBehalfOf": { - "reference": "Organization?identifier=https://github.com/synthetichealth/synthea|dd9914b0-9491-3330-a890-d34e95e497ea", - "display": "CHILD & FAMILY SERVICES, INC." - } - } ] - }, - "request": { - "method": "POST", - "url": "Provenance" - } - } ] -} diff --git a/LLMonFHIR/Resources/Mock Patients/Porfirio146_Jakubowski832_5b70be80-a0f2-849f-a286-8a8d2eab86b9.json.license b/LLMonFHIR/Resources/Mock Patients/Porfirio146_Jakubowski832_5b70be80-a0f2-849f-a286-8a8d2eab86b9.json.license deleted file mode 100644 index 750aeae..0000000 --- a/LLMonFHIR/Resources/Mock Patients/Porfirio146_Jakubowski832_5b70be80-a0f2-849f-a286-8a8d2eab86b9.json.license +++ /dev/null @@ -1,8 +0,0 @@ - -This source file is part of the Stanford LLM on FHIR project - -SPDX-FileCopyrightText: 2023 Stanford University - -SPDX-License-Identifier: MIT - -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/ResourceSelection.swift b/LLMonFHIR/Settings/ResourceSelection.swift index 176fb4b..ea34726 100644 --- a/LLMonFHIR/Settings/ResourceSelection.swift +++ b/LLMonFHIR/Settings/ResourceSelection.swift @@ -22,7 +22,11 @@ struct ResourceSelection: View { @MainActor var useHealthKitResources: Binding { Binding( get: { - standard.useHealthKitResources + if FeatureFlags.mockPatients { + showBundleSelection = true + return false + } + return standard.useHealthKitResources }, set: { newValue in showBundleSelection = !newValue @@ -38,7 +42,7 @@ struct ResourceSelection: View { Toggle(isOn: useHealthKitResources) { Text("Use HealthKit Resources") } - .onChange(of: useHealthKitResources.wrappedValue) { + .onChange(of: useHealthKitResources.wrappedValue, initial: true) { if useHealthKitResources.wrappedValue { _Concurrency.Task { await standard.loadHealthKitResources() diff --git a/LLMonFHIR/SharedContext/FeatureFlags.swift b/LLMonFHIR/SharedContext/FeatureFlags.swift index 7284411..0493eda 100644 --- a/LLMonFHIR/SharedContext/FeatureFlags.swift +++ b/LLMonFHIR/SharedContext/FeatureFlags.swift @@ -14,4 +14,6 @@ enum FeatureFlags { static let showOnboarding = CommandLine.arguments.contains("--showOnboarding") /// Sets the application in test mode static let testMode = CommandLine.arguments.contains("--testMode") + /// Use mock patients + static let mockPatients = CommandLine.arguments.contains("--mockPatients") } diff --git a/LLMonFHIRUITests/FHIRDisplayTests.swift b/LLMonFHIRUITests/FHIRDisplayTests.swift index fe69e35..2d4921b 100644 --- a/LLMonFHIRUITests/FHIRDisplayTests.swift +++ b/LLMonFHIRUITests/FHIRDisplayTests.swift @@ -13,11 +13,12 @@ final class FHIRDisplayTests: XCTestCase { override func setUpWithError() throws { try super.setUpWithError() - continueAfterFailure = false + // continueAfterFailure = false let app = XCUIApplication() - app.launchArguments = ["--skipOnboarding", "--testMode"] - app.deleteAndLaunch(withSpringboardAppName: "LLMonFHIR") + app.launchArguments = ["--skipOnboarding", "--testMode", "--mockPatients"] + app.launch() + // app.deleteAndLaunch(withSpringboardAppName: "LLMonFHIR") } func testFHIRResourcesView() throws { @@ -33,4 +34,67 @@ final class FHIRDisplayTests: XCTestCase { let newScreenMockResourceText = app.staticTexts["Mock Resource"] XCTAssertTrue(newScreenMockResourceText.exists, "The 'Mock Resource' text does not exist on the new screen.") } + + @MainActor + func testLLMOnFHIRPaperTest() async throws { + // throw XCTSkip() + + let app = XCUIApplication() + + let patients = [ + "Beatris270 Bogan287", + "Edythe31 Morar593", + "Gonzalo160 Duenas839", + "Jacklyn830 Veum823", + "Milton509 Ortiz186", + "Pasquale620 Kuhn96" + ] + + let questions = [ + "What are my current medications and how should I be taking them?", + "What are the most common side effects for each medication I am taking?", + "Am I allergic to any of my medications?", + "Can you summarize my current medical conditions?", + "What are the health behaviors I should be incorporating into my daily routine to help with my conditions?", + "Can you summarize my current medical conditions in German?", + "What are my recent laboratory values, what do they mean, and how can I improve them?" + ] + + for patient in patients { + app.navigationBars["Your Health Records"].buttons["Settings"].testExistanceAndTap() + app.staticTexts["Resources Selection"].testExistanceAndTap() + + app.buttons[patient].testExistanceAndTap(timeout: 20) + app.navigationBars["Resources Settings"].buttons["Settings"].testExistanceAndTap() + app.navigationBars["Settings"].buttons["Cancel"].testExistanceAndTap() + + app.buttons["Chat with all resources"].testExistanceAndTap() + + app.buttons["Reset Chat"].testExistanceAndTap() + + XCTAssertTrue(app.buttons["Close"].waitForExistence(timeout: 300)) + + for question in questions { + app.textViews["Message"].testExistanceAndTap() + app.typeText(question) + app.buttons["Send Message"].testExistanceAndTap() + + try await Task.sleep(for: .seconds(2)) + + XCTAssertTrue(app.buttons["Close"].waitForExistence(timeout: 300)) + } + + app.buttons["Close"].testExistanceAndTap() + + try await Task.sleep(for: .seconds(2)) + } + } +} + + +extension XCUIElement { + func testExistanceAndTap(timeout: Double = 2) { + XCTAssertTrue(waitForExistence(timeout: timeout)) + tap() + } } From 1d3597df3d18e11895ba93e89ede2c15a74531f2 Mon Sep 17 00:00:00 2001 From: Paul Schmiedmayer Date: Thu, 14 Dec 2023 19:08:49 -0800 Subject: [PATCH 2/6] Commit Changes --- LLMonFHIRUITests/FHIRDisplayTests.swift | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/LLMonFHIRUITests/FHIRDisplayTests.swift b/LLMonFHIRUITests/FHIRDisplayTests.swift index 2d4921b..f43a7c6 100644 --- a/LLMonFHIRUITests/FHIRDisplayTests.swift +++ b/LLMonFHIRUITests/FHIRDisplayTests.swift @@ -13,12 +13,12 @@ final class FHIRDisplayTests: XCTestCase { override func setUpWithError() throws { try super.setUpWithError() - // continueAfterFailure = false + continueAfterFailure = false let app = XCUIApplication() app.launchArguments = ["--skipOnboarding", "--testMode", "--mockPatients"] - app.launch() - // app.deleteAndLaunch(withSpringboardAppName: "LLMonFHIR") + + app.deleteAndLaunch(withSpringboardAppName: "LLMonFHIR") } func testFHIRResourcesView() throws { @@ -42,9 +42,9 @@ final class FHIRDisplayTests: XCTestCase { let app = XCUIApplication() let patients = [ - "Beatris270 Bogan287", - "Edythe31 Morar593", - "Gonzalo160 Duenas839", + // "Beatris270 Bogan287", + // "Edythe31 Morar593", + "Gonzalo160 Dueñas839", "Jacklyn830 Veum823", "Milton509 Ortiz186", "Pasquale620 Kuhn96" From 1e3b0de2b2c50e47b532c256a9d392edc8eb58de Mon Sep 17 00:00:00 2001 From: Paul Schmiedmayer Date: Thu, 14 Dec 2023 19:36:53 -0800 Subject: [PATCH 3/6] Update Patient Setup --- LLMonFHIR.xcodeproj/project.pbxproj | 8 +- .../FHIRMultipleResourceInterpreter.swift | 16 +- LLMonFHIR/Mock Data/MockData.swift | 34 +- LLMonFHIR/Resources/Localizable.xcstrings | 2 +- ..._ad134528-56a5-35fd-c37f-466ff119c625.json | 92122 ++++++++++++++++ ..._792a51c0-a2a4-ee26-c23c-7cb24f8a0e35.json | 28764 ----- LLMonFHIRUITests/FHIRDisplayTests.swift | 8 +- 7 files changed, 92158 insertions(+), 28796 deletions(-) create mode 100644 LLMonFHIR/Resources/Mock Patients/Allen322_Ferry570_ad134528-56a5-35fd-c37f-466ff119c625.json delete mode 100644 LLMonFHIR/Resources/Mock Patients/Pasquale620_Kuhn96_792a51c0-a2a4-ee26-c23c-7cb24f8a0e35.json diff --git a/LLMonFHIR.xcodeproj/project.pbxproj b/LLMonFHIR.xcodeproj/project.pbxproj index 38c7bee..a16e052 100644 --- a/LLMonFHIR.xcodeproj/project.pbxproj +++ b/LLMonFHIR.xcodeproj/project.pbxproj @@ -27,13 +27,13 @@ 2F4E23832989D51F0013F3D9 /* LLMonFHIRTestingSetup.swift in Sources */ = {isa = PBXBuildFile; fileRef = 2F4E23822989D51F0013F3D9 /* LLMonFHIRTestingSetup.swift */; }; 2F5BD9D12A78AAED0004E0AC /* String+LocalizedError.swift in Sources */ = {isa = PBXBuildFile; fileRef = 2F5BD9D02A78AAED0004E0AC /* String+LocalizedError.swift */; }; 2F5E32BD297E05EA003432F8 /* LLMonFHIRDelegate.swift in Sources */ = {isa = PBXBuildFile; fileRef = 2F5E32BC297E05EA003432F8 /* LLMonFHIRDelegate.swift */; }; + 2F6A880B2B2C0046002B9553 /* Allen322_Ferry570_ad134528-56a5-35fd-c37f-466ff119c625.json in Resources */ = {isa = PBXBuildFile; fileRef = 2F6A880A2B2C0046002B9553 /* Allen322_Ferry570_ad134528-56a5-35fd-c37f-466ff119c625.json */; }; 2F901CE22A1A03360007C167 /* SpeziOpenAI in Frameworks */ = {isa = PBXBuildFile; productRef = 2F901CE12A1A03360007C167 /* SpeziOpenAI */; }; 2FC186072AD52FE20065EBB2 /* SpeziSpeechSynthesizer in Frameworks */ = {isa = PBXBuildFile; productRef = 2FC186062AD52FE20065EBB2 /* SpeziSpeechSynthesizer */; }; 2FC186092AD52FFF0065EBB2 /* Localizable.xcstrings in Resources */ = {isa = PBXBuildFile; fileRef = 2FC186082AD52FFF0065EBB2 /* Localizable.xcstrings */; }; 2FC975A82978F11A00BA99FE /* Home.swift in Sources */ = {isa = PBXBuildFile; fileRef = 2FC975A72978F11A00BA99FE /* Home.swift */; }; 2FD024892B116EEF009A682C /* LLMFunction.swift in Sources */ = {isa = PBXBuildFile; fileRef = 2FD024882B116EEF009A682C /* LLMFunction.swift */; }; 2FD0248B2B116EF6009A682C /* LLMStreamResult.swift in Sources */ = {isa = PBXBuildFile; fileRef = 2FD0248A2B116EF6009A682C /* LLMStreamResult.swift */; }; - 2FD024902B1171EC009A682C /* Pasquale620_Kuhn96_792a51c0-a2a4-ee26-c23c-7cb24f8a0e35.json in Resources */ = {isa = PBXBuildFile; fileRef = 2FD0248C2B1171EC009A682C /* Pasquale620_Kuhn96_792a51c0-a2a4-ee26-c23c-7cb24f8a0e35.json */; }; 2FD024912B1171EC009A682C /* Edythe31_Morar593_9c3df38a-d3b7-2198-3898-51f9153d023d.json in Resources */ = {isa = PBXBuildFile; fileRef = 2FD0248D2B1171EC009A682C /* Edythe31_Morar593_9c3df38a-d3b7-2198-3898-51f9153d023d.json */; }; 2FD024922B1171EC009A682C /* Milton509_Ortiz186_d66b5418-06cb-fc8a-8c13-85685b6ac939.json in Resources */ = {isa = PBXBuildFile; fileRef = 2FD0248E2B1171EC009A682C /* Milton509_Ortiz186_d66b5418-06cb-fc8a-8c13-85685b6ac939.json */; }; 2FD8E8272A1AAD9B00357F4E /* LLMonFHIRStandard.swift in Sources */ = {isa = PBXBuildFile; fileRef = 2FD8E8262A1AAD9B00357F4E /* LLMonFHIRStandard.swift */; }; @@ -97,13 +97,13 @@ 2F4E23822989D51F0013F3D9 /* LLMonFHIRTestingSetup.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = LLMonFHIRTestingSetup.swift; sourceTree = ""; }; 2F5BD9D02A78AAED0004E0AC /* String+LocalizedError.swift */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.swift; path = "String+LocalizedError.swift"; sourceTree = ""; }; 2F5E32BC297E05EA003432F8 /* LLMonFHIRDelegate.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = LLMonFHIRDelegate.swift; sourceTree = ""; }; + 2F6A880A2B2C0046002B9553 /* Allen322_Ferry570_ad134528-56a5-35fd-c37f-466ff119c625.json */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text.json; path = "Allen322_Ferry570_ad134528-56a5-35fd-c37f-466ff119c625.json"; sourceTree = ""; }; 2FAEC07F297F583900C11C42 /* LLMonFHIR.entitlements */ = {isa = PBXFileReference; lastKnownFileType = text.plist.entitlements; path = LLMonFHIR.entitlements; sourceTree = ""; }; 2FC186082AD52FFF0065EBB2 /* Localizable.xcstrings */ = {isa = PBXFileReference; lastKnownFileType = text.json.xcstrings; path = Localizable.xcstrings; sourceTree = ""; }; 2FC94CD4298B0A1D009C8209 /* LLMonFHIR.xctestplan */ = {isa = PBXFileReference; lastKnownFileType = text; path = LLMonFHIR.xctestplan; sourceTree = ""; }; 2FC975A72978F11A00BA99FE /* Home.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = Home.swift; sourceTree = ""; }; 2FD024882B116EEF009A682C /* LLMFunction.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = LLMFunction.swift; sourceTree = ""; }; 2FD0248A2B116EF6009A682C /* LLMStreamResult.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = LLMStreamResult.swift; sourceTree = ""; }; - 2FD0248C2B1171EC009A682C /* Pasquale620_Kuhn96_792a51c0-a2a4-ee26-c23c-7cb24f8a0e35.json */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text.json; path = "Pasquale620_Kuhn96_792a51c0-a2a4-ee26-c23c-7cb24f8a0e35.json"; sourceTree = ""; }; 2FD0248D2B1171EC009A682C /* Edythe31_Morar593_9c3df38a-d3b7-2198-3898-51f9153d023d.json */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text.json; path = "Edythe31_Morar593_9c3df38a-d3b7-2198-3898-51f9153d023d.json"; sourceTree = ""; }; 2FD0248E2B1171EC009A682C /* Milton509_Ortiz186_d66b5418-06cb-fc8a-8c13-85685b6ac939.json */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text.json; path = "Milton509_Ortiz186_d66b5418-06cb-fc8a-8c13-85685b6ac939.json"; sourceTree = ""; }; 2FD8E8262A1AAD9B00357F4E /* LLMonFHIRStandard.swift */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.swift; path = LLMonFHIRStandard.swift; sourceTree = ""; }; @@ -174,12 +174,12 @@ 2F036EBC2B0EEAD9009B2745 /* Mock Patients */ = { isa = PBXGroup; children = ( + 2F6A880A2B2C0046002B9553 /* Allen322_Ferry570_ad134528-56a5-35fd-c37f-466ff119c625.json */, 2F036EAF2B0EEAD6009B2745 /* Beatris270_Bogan287_5b3645de-a2d0-d016-0839-bab3757c4c58.json */, 2FD0248D2B1171EC009A682C /* Edythe31_Morar593_9c3df38a-d3b7-2198-3898-51f9153d023d.json */, 2F036EAB2B0EEAD5009B2745 /* Gonzalo160_Duenas839_ed70a28f-30b2-acb7-658a-8b340dadd685.json */, 2F036EAA2B0EEAD5009B2745 /* Jacklyn830_Veum823_e0e1f21a-22a7-d166-7bb1-63f6bbce1a32.json */, 2FD0248E2B1171EC009A682C /* Milton509_Ortiz186_d66b5418-06cb-fc8a-8c13-85685b6ac939.json */, - 2FD0248C2B1171EC009A682C /* Pasquale620_Kuhn96_792a51c0-a2a4-ee26-c23c-7cb24f8a0e35.json */, ); path = "Mock Patients"; sourceTree = ""; @@ -485,7 +485,7 @@ buildActionMask = 2147483647; files = ( 653A255528338800005D4D48 /* Assets.xcassets in Resources */, - 2FD024902B1171EC009A682C /* Pasquale620_Kuhn96_792a51c0-a2a4-ee26-c23c-7cb24f8a0e35.json in Resources */, + 2F6A880B2B2C0046002B9553 /* Allen322_Ferry570_ad134528-56a5-35fd-c37f-466ff119c625.json in Resources */, 2FD024912B1171EC009A682C /* Edythe31_Morar593_9c3df38a-d3b7-2198-3898-51f9153d023d.json in Resources */, 2F036EB42B0EEAD6009B2745 /* Jacklyn830_Veum823_e0e1f21a-22a7-d166-7bb1-63f6bbce1a32.json in Resources */, 2F036EB52B0EEAD6009B2745 /* Gonzalo160_Duenas839_ed70a28f-30b2-acb7-658a-8b340dadd685.json in Resources */, diff --git a/LLMonFHIR/FHIR Interpretation/FHIRMultipleResourceInterpreter.swift b/LLMonFHIR/FHIR Interpretation/FHIRMultipleResourceInterpreter.swift index d789950..09314a3 100644 --- a/LLMonFHIR/FHIR Interpretation/FHIRMultipleResourceInterpreter.swift +++ b/LLMonFHIR/FHIR Interpretation/FHIRMultipleResourceInterpreter.swift @@ -79,19 +79,23 @@ class FHIRMultipleResourceInterpreter { } private func prepareSystemPrompt() { - var prompt = FHIRPrompt.interpretMultipleResources.prompt - if let patient = fhirStore.patient { - prompt.append(patient.jsonDescription) - } - if chat.isEmpty { chat = [ Chat( role: .system, - content: prompt + content: FHIRPrompt.interpretMultipleResources.prompt ) ] } + + if let patient = fhirStore.patient { + chat.append( + Chat( + role: .system, + content: patient.jsonDescription + ) + ) + } } private func executeLLMQueries() async throws { diff --git a/LLMonFHIR/Mock Data/MockData.swift b/LLMonFHIR/Mock Data/MockData.swift index e193a7d..5f45c8d 100644 --- a/LLMonFHIR/Mock Data/MockData.swift +++ b/LLMonFHIR/Mock Data/MockData.swift @@ -12,6 +12,21 @@ import SpeziFHIRMockPatients extension ModelsR4.Bundle { + private static var _allen322Ferry570: ModelsR4.Bundle? + static var allen322Ferry570: ModelsR4.Bundle { + get async { + if let allen322Ferry570 = _allen322Ferry570 { + return allen322Ferry570 + } + + let allen322Ferry570 = await Foundation.Bundle.main.loadFHIRBundle( + withName: "Allen322_Ferry570_ad134528-56a5-35fd-c37f-466ff119c625" + ) + ModelsR4.Bundle._allen322Ferry570 = allen322Ferry570 + return allen322Ferry570 + } + } + private static var _beatris270Bogan287: ModelsR4.Bundle? static var beatris270Bogan287: ModelsR4.Bundle { get async { @@ -87,31 +102,16 @@ extension ModelsR4.Bundle { } } - private static var _pasquale620Kuhn96: ModelsR4.Bundle? - static var pasquale620Kuhn96: ModelsR4.Bundle { - get async { - if let pasquale620Kuhn96 = _pasquale620Kuhn96 { - return pasquale620Kuhn96 - } - - let pasquale620Kuhn96 = await Foundation.Bundle.main.loadFHIRBundle( - withName: "Pasquale620_Kuhn96_792a51c0-a2a4-ee26-c23c-7cb24f8a0e35" - ) - ModelsR4.Bundle._pasquale620Kuhn96 = pasquale620Kuhn96 - return pasquale620Kuhn96 - } - } - static var llmOnFHIRMockPatients: [Bundle] { get async { await [ + .allen322Ferry570, .beatris270Bogan287, .edythe31Morar593, .gonzalo160Duenas839, .jacklyn830Veum823, - .milton509Ortiz186, - .pasquale620Kuhn96 + .milton509Ortiz186 ] } } diff --git a/LLMonFHIR/Resources/Localizable.xcstrings b/LLMonFHIR/Resources/Localizable.xcstrings index c71563d..b5ca30e 100644 --- a/LLMonFHIR/Resources/Localizable.xcstrings +++ b/LLMonFHIR/Resources/Localizable.xcstrings @@ -1195,7 +1195,7 @@ "en" : { "stringUnit" : { "state" : "translated", - "value" : "You are the LLM on FHIR application. Your 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. Leave out any technical details like JSON, FHIR resources, and other implementation details of the underlying data resources.\nOnly request relevant resources and focus on recent resources. Try to reduce the number of requested resources to a reasonable scope.\nE.g. if the user asks about their Medication it would be recommended to request all MedicationRequest FHIR resource types.\n\nInterpret the resources by explaining the data relevant to the user's health. Explain the relevant medical context in a language understandable by a user who is not a medical professional, ideally at a 5th-grade reading level. You 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 based on the FHIR patient resources if available to start the conversation. You may already request FHIR resources using the \"get_resources\" function. The initial summary should be short and simple and NOT list the records' titles or any resource's detailed content; stay at a high level. End 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. Make sure your response is in the same language the user writes to you in. The tense should be present.\n\nThe patient resource is provided as the initial context. Ensure to leave out any like SSN, passport number, and telephone number." + "value" : "You are the LLM on FHIR application. Your 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. Leave out any technical details like JSON, FHIR resources, and other implementation details of the underlying data resources.\nOnly request relevant resources and focus on recent resources. Try to reduce the number of requested resources to a reasonable scope.\nE.g. if the user asks about their Medication it would be recommended to request all MedicationRequest FHIR resource types.\n\nInterpret the resources by explaining the data relevant to the user's health. Explain the relevant medical context in a language understandable by a user who is not a medical professional, ideally at a 5th-grade reading level. You should provide factual and precise information in a compact summary in short responses.\n\nThe patient resource is provided as the initial context. Ensure to leave out any like SSN, passport number, and telephone number. \nDo not introduce yourself at the beginning and immediately return a summary of the user based on the FHIR patient resources. No not request any FHIR resources using the \"get_resources\" function for your first message. The initial summary should be short and simple; stay at a high level. End with a question asking the user if they have any questions. Make sure your response is in the same language the user writes to you in, not the one stated in the patient resource. The tense should be present." } } } diff --git a/LLMonFHIR/Resources/Mock Patients/Allen322_Ferry570_ad134528-56a5-35fd-c37f-466ff119c625.json b/LLMonFHIR/Resources/Mock Patients/Allen322_Ferry570_ad134528-56a5-35fd-c37f-466ff119c625.json new file mode 100644 index 0000000..1966cd2 --- /dev/null +++ b/LLMonFHIR/Resources/Mock Patients/Allen322_Ferry570_ad134528-56a5-35fd-c37f-466ff119c625.json @@ -0,0 +1,92122 @@ +{ + "resourceType": "Bundle", + "type": "transaction", + "entry": [ { + "fullUrl": "urn:uuid:ad134528-56a5-35fd-c37f-466ff119c625", + "resource": { + "resourceType": "Patient", + "id": "ad134528-56a5-35fd-c37f-466ff119c625", + "meta": { + "profile": [ "http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient" ] + }, + "text": { + "status": "generated", + "div": "
Generated by Synthea.Version identifier: master-branch-latest-7-gcc27279b\n . Person seed: 8618715897759963534 Population seed: 0
" + }, + "extension": [ { + "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race", + "extension": [ { + "url": "ombCategory", + "valueCoding": { + "system": "urn:oid:2.16.840.1.113883.6.238", + "code": "2106-3", + "display": "White" + } + }, { + "url": "text", + "valueString": "White" + } ] + }, { + "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity", + "extension": [ { + "url": "ombCategory", + "valueCoding": { + "system": "urn:oid:2.16.840.1.113883.6.238", + "code": "2186-5", + "display": "Not Hispanic or Latino" + } + }, { + "url": "text", + "valueString": "Not Hispanic or Latino" + } ] + }, { + "url": "http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName", + "valueString": "Jinny850 Pouros728" + }, { + "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex", + "valueCode": "M" + }, { + "url": "http://hl7.org/fhir/StructureDefinition/patient-birthPlace", + "valueAddress": { + "city": "Millis", + "state": "Massachusetts", + "country": "US" + } + }, { + "url": "http://synthetichealth.github.io/synthea/disability-adjusted-life-years", + "valueDecimal": 18.902413381088788 + }, { + "url": "http://synthetichealth.github.io/synthea/quality-adjusted-life-years", + "valueDecimal": 61.09758661891121 + } ], + "identifier": [ { + "system": "https://github.com/synthetichealth/synthea", + "value": "ad134528-56a5-35fd-c37f-466ff119c625" + }, { + "type": { + "coding": [ { + "system": "http://terminology.hl7.org/CodeSystem/v2-0203", + "code": "MR", + "display": "Medical Record Number" + } ], + "text": "Medical Record Number" + }, + "system": "http://hospital.smarthealthit.org", + "value": "ad134528-56a5-35fd-c37f-466ff119c625" + }, { + "type": { + "coding": [ { + "system": "http://terminology.hl7.org/CodeSystem/v2-0203", + "code": "SS", + "display": "Social Security Number" + } ], + "text": "Social Security Number" + }, + "system": "http://hl7.org/fhir/sid/us-ssn", + "value": "999-98-4342" + }, { + "type": { + "coding": [ { + "system": "http://terminology.hl7.org/CodeSystem/v2-0203", + "code": "DL", + "display": "Driver's License" + } ], + "text": "Driver's License" + }, + "system": "urn:oid:2.16.840.1.113883.4.3.25", + "value": "S99946280" + }, { + "type": { + "coding": [ { + "system": "http://terminology.hl7.org/CodeSystem/v2-0203", + "code": "PPN", + "display": "Passport Number" + } ], + "text": "Passport Number" + }, + "system": "http://standardhealthrecord.org/fhir/StructureDefinition/passportNumber", + "value": "X84186192X" + } ], + "name": [ { + "use": "official", + "family": "Ferry570", + "given": [ "Allen322" ], + "prefix": [ "Mr." ] + } ], + "telecom": [ { + "system": "phone", + "value": "555-503-8314", + "use": "home" + } ], + "gender": "male", + "birthDate": "1940-12-31", + "address": [ { + "extension": [ { + "url": "http://hl7.org/fhir/StructureDefinition/geolocation", + "extension": [ { + "url": "latitude", + "valueDecimal": 42.333816171984 + }, { + "url": 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}, { - "reference": "urn:uuid:1ac82493-0b8f-f353-abb4-8fb48e18b723" - }, { - "reference": "urn:uuid:9eba72e4-f827-b0d2-c991-8699e442e1ad" - }, { - "reference": "urn:uuid:b89e830f-caee-86be-444e-53375372459b" - }, { - "reference": "urn:uuid:0b370c55-7b84-8559-f766-22de15f7a803" - }, { - "reference": "urn:uuid:e1004f15-7bd0-e5fb-4aa0-b86bade67c33" - }, { - "reference": "urn:uuid:bf4f5cbb-751a-7f25-0835-d0cf002547e5" - }, { - "reference": "urn:uuid:1e4379d9-292a-e5d5-5a23-cbc79aa396b2" - }, { - "reference": "urn:uuid:cd68fe91-3571-d01b-e341-9cf1273730c4" - }, { - "reference": "urn:uuid:20ff5935-e763-8cec-5a90-4901368988d0" - } ], - "recorded": "2021-11-22T01:35:08.996-05:00", - "agent": [ { - "type": { - "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/provenance-participant-type", - "code": "author", - "display": "Author" - } ], - "text": "Author" - }, - "who": { - "reference": "Practitioner?identifier=http://hl7.org/fhir/sid/us-npi|9999955339", - "display": "Dr. Jose871 DuBuque211" - }, - "onBehalfOf": { - "reference": "Organization?identifier=https://github.com/synthetichealth/synthea|99157068-4f0d-3906-8723-d8b7fda349f5", - "display": "PCP107381" - } - }, { - "type": { - "coding": [ { - "system": "http://hl7.org/fhir/us/core/CodeSystem/us-core-provenance-participant-type", - "code": "transmitter", - "display": "Transmitter" - } ], - "text": "Transmitter" - }, - "who": { - "reference": "Practitioner?identifier=http://hl7.org/fhir/sid/us-npi|9999955339", - "display": "Dr. Jose871 DuBuque211" - }, - "onBehalfOf": { - "reference": "Organization?identifier=https://github.com/synthetichealth/synthea|99157068-4f0d-3906-8723-d8b7fda349f5", - "display": "PCP107381" - } - } ] - }, - "request": { - "method": "POST", - "url": "Provenance" - } - } ] -} diff --git a/LLMonFHIRUITests/FHIRDisplayTests.swift b/LLMonFHIRUITests/FHIRDisplayTests.swift index f43a7c6..bd5e6a2 100644 --- a/LLMonFHIRUITests/FHIRDisplayTests.swift +++ b/LLMonFHIRUITests/FHIRDisplayTests.swift @@ -42,12 +42,12 @@ final class FHIRDisplayTests: XCTestCase { let app = XCUIApplication() let patients = [ - // "Beatris270 Bogan287", - // "Edythe31 Morar593", + "Allen322 Ferry570", + "Beatris270 Bogan287", + "Edythe31 Morar593", "Gonzalo160 Dueñas839", "Jacklyn830 Veum823", - "Milton509 Ortiz186", - "Pasquale620 Kuhn96" + "Milton509 Ortiz186" ] let questions = [ From 6f55483bfc5a7bc2f594c844151f4f256bbd19ab Mon Sep 17 00:00:00 2001 From: Paul Schmiedmayer Date: Thu, 14 Dec 2023 19:38:01 -0800 Subject: [PATCH 4/6] Update Patients --- LLMonFHIRUITests/FHIRDisplayTests.swift | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/LLMonFHIRUITests/FHIRDisplayTests.swift b/LLMonFHIRUITests/FHIRDisplayTests.swift index bd5e6a2..1a17a41 100644 --- a/LLMonFHIRUITests/FHIRDisplayTests.swift +++ b/LLMonFHIRUITests/FHIRDisplayTests.swift @@ -42,12 +42,12 @@ final class FHIRDisplayTests: XCTestCase { let app = XCUIApplication() let patients = [ - "Allen322 Ferry570", - "Beatris270 Bogan287", - "Edythe31 Morar593", - "Gonzalo160 Dueñas839", - "Jacklyn830 Veum823", - "Milton509 Ortiz186" + "Allen322 Ferry570", // @Paul + "Beatris270 Bogan287", // @Paul + "Edythe31 Morar593", // @Paul + "Gonzalo160 Dueñas839", // @Vishnu + "Jacklyn830 Veum823", // @Vishnu + "Milton509 Ortiz186" // @Vishnu ] let questions = [ From 9de7dc28b82c1915aca793f35fbe704b7aadeacd Mon Sep 17 00:00:00 2001 From: Paul Schmiedmayer Date: Thu, 14 Dec 2023 22:16:39 -0800 Subject: [PATCH 5/6] Update Setup --- .../FHIR Display/MultipleResourcesChatView.swift | 1 + LLMonFHIRUITests/FHIRDisplayTests.swift | 14 +++++++------- 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/LLMonFHIR/FHIR Display/MultipleResourcesChatView.swift b/LLMonFHIR/FHIR Display/MultipleResourcesChatView.swift index c05dd0a..5e21c4e 100644 --- a/LLMonFHIR/FHIR Display/MultipleResourcesChatView.swift +++ b/LLMonFHIR/FHIR Display/MultipleResourcesChatView.swift @@ -89,6 +89,7 @@ struct MultipleResourcesChatView: View { .accessibilityLabel(Text("Reset Chat")) } ) + .disabled(multipleResourceInterpreter.viewState == .processing) } } } diff --git a/LLMonFHIRUITests/FHIRDisplayTests.swift b/LLMonFHIRUITests/FHIRDisplayTests.swift index 1a17a41..ff8eda5 100644 --- a/LLMonFHIRUITests/FHIRDisplayTests.swift +++ b/LLMonFHIRUITests/FHIRDisplayTests.swift @@ -37,17 +37,17 @@ final class FHIRDisplayTests: XCTestCase { @MainActor func testLLMOnFHIRPaperTest() async throws { - // throw XCTSkip() + throw XCTSkip() let app = XCUIApplication() let patients = [ - "Allen322 Ferry570", // @Paul - "Beatris270 Bogan287", // @Paul - "Edythe31 Morar593", // @Paul - "Gonzalo160 Dueñas839", // @Vishnu - "Jacklyn830 Veum823", // @Vishnu - "Milton509 Ortiz186" // @Vishnu + "Allen322 Ferry570", + "Beatris270 Bogan287", + "Edythe31 Morar593", + "Gonzalo160 Dueñas839", + "Jacklyn830 Veum823", + "Milton509 Ortiz186" ] let questions = [ From 81023b94fb34f8ff914e6ed86d3d2ed252a1085e Mon Sep 17 00:00:00 2001 From: Paul Schmiedmayer Date: Thu, 14 Dec 2023 22:17:51 -0800 Subject: [PATCH 6/6] Update Setup --- ...22_Ferry570_ad134528-56a5-35fd-c37f-466ff119c625.json.license} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename LLMonFHIR/Resources/Mock Patients/{Pasquale620_Kuhn96_792a51c0-a2a4-ee26-c23c-7cb24f8a0e35.json.license => Allen322_Ferry570_ad134528-56a5-35fd-c37f-466ff119c625.json.license} (100%) diff --git a/LLMonFHIR/Resources/Mock Patients/Pasquale620_Kuhn96_792a51c0-a2a4-ee26-c23c-7cb24f8a0e35.json.license b/LLMonFHIR/Resources/Mock Patients/Allen322_Ferry570_ad134528-56a5-35fd-c37f-466ff119c625.json.license similarity index 100% rename from LLMonFHIR/Resources/Mock Patients/Pasquale620_Kuhn96_792a51c0-a2a4-ee26-c23c-7cb24f8a0e35.json.license rename to LLMonFHIR/Resources/Mock Patients/Allen322_Ferry570_ad134528-56a5-35fd-c37f-466ff119c625.json.license