From 4dfd4f18e92865b8cb94998ed693ebcead343c8d Mon Sep 17 00:00:00 2001 From: Paul Schmiedmayer Date: Wed, 18 Sep 2024 10:05:23 -0700 Subject: [PATCH 1/3] Update README --- ...y570_ad134528-56a5-35fd-c37f-466ff119c625.json.license | 8 -------- ...n287_5b3645de-a2d0-d016-0839-bab3757c4c58.json.license | 8 -------- ...r593_9c3df38a-d3b7-2198-3898-51f9153d023d.json.license | 8 -------- ...s839_ed70a28f-30b2-acb7-658a-8b340dadd685.json.license | 8 -------- ...m823_e0e1f21a-22a7-d166-7bb1-63f6bbce1a32.json.license | 8 -------- ...z186_d66b5418-06cb-fc8a-8c13-85685b6ac939.json.license | 8 -------- README.md | 2 ++ 7 files changed, 2 insertions(+), 48 deletions(-) delete mode 100644 LLMonFHIR/Resources/Mock Patients/Allen322_Ferry570_ad134528-56a5-35fd-c37f-466ff119c625.json.license delete mode 100644 LLMonFHIR/Resources/Mock Patients/Beatris270_Bogan287_5b3645de-a2d0-d016-0839-bab3757c4c58.json.license delete mode 100644 LLMonFHIR/Resources/Mock Patients/Edythe31_Morar593_9c3df38a-d3b7-2198-3898-51f9153d023d.json.license delete mode 100644 LLMonFHIR/Resources/Mock Patients/Gonzalo160_Duenas839_ed70a28f-30b2-acb7-658a-8b340dadd685.json.license delete mode 100644 LLMonFHIR/Resources/Mock Patients/Jacklyn830_Veum823_e0e1f21a-22a7-d166-7bb1-63f6bbce1a32.json.license delete mode 100644 LLMonFHIR/Resources/Mock Patients/Milton509_Ortiz186_d66b5418-06cb-fc8a-8c13-85685b6ac939.json.license diff --git a/LLMonFHIR/Resources/Mock Patients/Allen322_Ferry570_ad134528-56a5-35fd-c37f-466ff119c625.json.license b/LLMonFHIR/Resources/Mock Patients/Allen322_Ferry570_ad134528-56a5-35fd-c37f-466ff119c625.json.license deleted file mode 100644 index 750aeae..0000000 --- a/LLMonFHIR/Resources/Mock Patients/Allen322_Ferry570_ad134528-56a5-35fd-c37f-466ff119c625.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/Beatris270_Bogan287_5b3645de-a2d0-d016-0839-bab3757c4c58.json.license b/LLMonFHIR/Resources/Mock Patients/Beatris270_Bogan287_5b3645de-a2d0-d016-0839-bab3757c4c58.json.license deleted file mode 100644 index 750aeae..0000000 --- a/LLMonFHIR/Resources/Mock Patients/Beatris270_Bogan287_5b3645de-a2d0-d016-0839-bab3757c4c58.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/Edythe31_Morar593_9c3df38a-d3b7-2198-3898-51f9153d023d.json.license b/LLMonFHIR/Resources/Mock Patients/Edythe31_Morar593_9c3df38a-d3b7-2198-3898-51f9153d023d.json.license deleted file mode 100644 index 750aeae..0000000 --- a/LLMonFHIR/Resources/Mock Patients/Edythe31_Morar593_9c3df38a-d3b7-2198-3898-51f9153d023d.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/Gonzalo160_Duenas839_ed70a28f-30b2-acb7-658a-8b340dadd685.json.license b/LLMonFHIR/Resources/Mock Patients/Gonzalo160_Duenas839_ed70a28f-30b2-acb7-658a-8b340dadd685.json.license deleted file mode 100644 index 750aeae..0000000 --- a/LLMonFHIR/Resources/Mock Patients/Gonzalo160_Duenas839_ed70a28f-30b2-acb7-658a-8b340dadd685.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/Jacklyn830_Veum823_e0e1f21a-22a7-d166-7bb1-63f6bbce1a32.json.license b/LLMonFHIR/Resources/Mock Patients/Jacklyn830_Veum823_e0e1f21a-22a7-d166-7bb1-63f6bbce1a32.json.license deleted file mode 100644 index 750aeae..0000000 --- a/LLMonFHIR/Resources/Mock Patients/Jacklyn830_Veum823_e0e1f21a-22a7-d166-7bb1-63f6bbce1a32.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/Milton509_Ortiz186_d66b5418-06cb-fc8a-8c13-85685b6ac939.json.license b/LLMonFHIR/Resources/Mock Patients/Milton509_Ortiz186_d66b5418-06cb-fc8a-8c13-85685b6ac939.json.license deleted file mode 100644 index 750aeae..0000000 --- a/LLMonFHIR/Resources/Mock Patients/Milton509_Ortiz186_d66b5418-06cb-fc8a-8c13-85685b6ac939.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/README.md b/README.md index e9d8408..e5969da 100644 --- a/README.md +++ b/README.md @@ -63,6 +63,8 @@ LLM on FHIR requires access to the FHIR health records stored in the Apple Healt In case no health records are available, please follow the instructions to connect and retrieve your health records from your provider. If your health records are visible in the Apple Health app, please ensure that LLM on FHIR 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. +> [!TIP] +> You can also use a set of [Synthea](https://doi.org/10.1093/jamia/ocx079)-based patients loaded from [SpeziFHIR](https://github.com/StanfordSpezi/SpeziFHIR) ([SpeziFHIRMockPatients](https://github.com/StanfordSpezi/SpeziFHIR/tree/main/Sources/SpeziFHIRMockPatients)) to test out the application without the need to connect it to HealthKit. You can select the synthetic patients in the account settings view of the application. ## Application Structure From 699435564aafb82b037c30bb35df0d9844195c43 Mon Sep 17 00:00:00 2001 From: Paul Schmiedmayer Date: Wed, 18 Sep 2024 10:08:35 -0700 Subject: [PATCH 2/3] Update CodeQL Action as Swift 6 is not yet supported --- .github/workflows/build-and-test.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/build-and-test.yml b/.github/workflows/build-and-test.yml index bcd848b..8d299da 100644 --- a/.github/workflows/build-and-test.yml +++ b/.github/workflows/build-and-test.yml @@ -26,6 +26,7 @@ jobs: with: codeql: true fastlanelane: codeql + xcodeversion: '15.4' permissions: security-events: write actions: read From 39b367a67b0ac76b0633016d4035756e9d143735 Mon Sep 17 00:00:00 2001 From: Vishnu Ravi Date: Sat, 28 Dec 2024 22:44:07 -0500 Subject: [PATCH 3/3] Re-run actions --- LLMonFHIR.xcodeproj/project.pbxproj | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/LLMonFHIR.xcodeproj/project.pbxproj b/LLMonFHIR.xcodeproj/project.pbxproj index 09a0268..eb8cb0d 100644 --- a/LLMonFHIR.xcodeproj/project.pbxproj +++ b/LLMonFHIR.xcodeproj/project.pbxproj @@ -1114,7 +1114,7 @@ repositoryURL = "https://github.com/StanfordSpezi/SpeziLLM"; requirement = { kind = upToNextMinorVersion; - minimumVersion = 0.8.1; + minimumVersion = 0.8.3; }; }; 97BBC2912B8C6BCA009EE6D9 /* XCRemoteSwiftPackageReference "SpeziFHIR" */ = {