Add LLM functionality from SpeziFHIR

.github/workflows/build-and-test.yml

@@ -26,7 +26,6 @@ jobs:
     with:
       codeql: true
       fastlanelane: codeql
-      xcodeversion: '15.4'
     permissions:
       security-events: write
       actions: read

LLMonFHIR.xcodeproj/project.xcworkspace/xcshareddata/swiftpm/Package.resolved

@@ -1,31 +1,58 @@
 {
-  "originHash" : "ba25e03f96176869eb16eff816add82265b9f18b602261a3f50d9822f350899a",
+  "originHash" : "8525584d8580a0805dcd07acbb93dcce1d6c409f970b4c38d165d5a63cd5b251",
   "pins" : [
     {
       "identity" : "fhirmodels",
       "kind" : "remoteSourceControl",
       "location" : "https://github.com/apple/FHIRModels",
       "state" : {
-        "revision" : "861afd5816a98d38f86220eab2f812d76cad84a0",
-        "version" : "0.5.0"
+        "revision" : "ee8b55c245e92389e05b0a56ad2b84d37c1985e5",
+        "version" : "0.6.1"
+      }
+    },
+    {
+      "identity" : "gzipswift",
+      "kind" : "remoteSourceControl",
+      "location" : "https://github.com/1024jp/GzipSwift",
+      "state" : {
+        "revision" : "731037f6cc2be2ec01562f6597c1d0aa3fe6fd05",
+        "version" : "6.0.1"
       }
     },
     {
       "identity" : "healthkitonfhir",
       "kind" : "remoteSourceControl",
       "location" : "https://github.com/StanfordBDHG/HealthKitOnFHIR.git",
       "state" : {
-        "revision" : "b0cfe35a2263a517b22196b559d2dd1d1e2afcd9",
-        "version" : "0.2.9"
+        "revision" : "87a9257e6fa37407f3437e4a0bf21dd09a4ea7c5",
+        "version" : "0.2.11"
+      }
+    },
+    {
+      "identity" : "jinja",
+      "kind" : "remoteSourceControl",
+      "location" : "https://github.com/maiqingqiang/Jinja",
+      "state" : {
+        "revision" : "6dbe4c449469fb586d0f7339f900f0dd4d78b167",
+        "version" : "1.0.6"
+      }
+    },
+    {
+      "identity" : "mlx-swift",
+      "kind" : "remoteSourceControl",
+      "location" : "https://github.com/ml-explore/mlx-swift",
+      "state" : {
+        "revision" : "70dbb62128a5a1471a5ab80363430adb33470cab",
+        "version" : "0.21.2"
       }
     },
     {
-      "identity" : "llama.cpp",
+      "identity" : "mlx-swift-examples",
       "kind" : "remoteSourceControl",
-      "location" : "https://github.com/StanfordBDHG/llama.cpp",
+      "location" : "https://github.com/ml-explore/mlx-swift-examples",
       "state" : {
-        "revision" : "6839853a321778906e210a33ee2c6aec52f34c97",
-        "version" : "0.3.3"
+        "revision" : "7baf9bc2d7a2b68b4bfcae308e448ec68b8ef049",
+        "version" : "1.18.1"
       }
     },
     {
@@ -42,53 +69,53 @@
       "kind" : "remoteSourceControl",
       "location" : "https://github.com/StanfordSpezi/Spezi",
       "state" : {
-        "revision" : "c43e4fa3d3938a847de2b677091a34ddaea5bc76",
-        "version" : "1.2.3"
+        "revision" : "4513a697572e8e1faea1e0ee52e6fad4b8d3dd8d",
+        "version" : "1.8.0"
       }
     },
     {
       "identity" : "spezichat",
       "kind" : "remoteSourceControl",
       "location" : "https://github.com/StanfordSpezi/SpeziChat",
       "state" : {
-        "revision" : "aaa10d71431b78ece8bf29f95c0050632714984d",
-        "version" : "0.2.0"
+        "revision" : "940ffbec504849968305d9f956344a4f35b6cd48",
+        "version" : "0.2.1"
       }
     },
     {
       "identity" : "spezifhir",
       "kind" : "remoteSourceControl",
       "location" : "https://github.com/StanfordSpezi/SpeziFHIR",
       "state" : {
-        "revision" : "4357bd22bfe3b27bd9beec52330bca62d10ee202",
-        "version" : "0.6.2"
+        "revision" : "a2e68a2e8d2f86dbe03c52ba4f9a99dbbcf137fa",
+        "version" : "0.7.0"
       }
     },
     {
       "identity" : "spezifoundation",
       "kind" : "remoteSourceControl",
       "location" : "https://github.com/StanfordSpezi/SpeziFoundation",
       "state" : {
-        "revision" : "4781d96a09587f3d47ac3f3e71d197149b288146",
-        "version" : "1.1.3"
+        "revision" : "5b4ad1b343154b52a68c33a6bfe02d9cb07cb9dc",
+        "version" : "2.0.0"
       }
     },
     {
       "identity" : "spezihealthkit",
       "kind" : "remoteSourceControl",
       "location" : "https://github.com/StanfordSpezi/SpeziHealthKit.git",
       "state" : {
-        "revision" : "1e9cb5a6036ac7f4ff37ea1c3ed4898103339ad1",
-        "version" : "0.5.3"
+        "revision" : "fbdec78fcb2f90d6338f1968e21dd11fbee65070",
+        "version" : "0.6.0"
       }
     },
     {
       "identity" : "spezillm",
       "kind" : "remoteSourceControl",
       "location" : "https://github.com/StanfordSpezi/SpeziLLM",
       "state" : {
-        "revision" : "3663884f23e55c67c875a97c5da08ed172ea02ac",
-        "version" : "0.8.3"
+        "revision" : "26b1e07756556b1b329f3a9a3267a5f99c0c2e78",
+        "version" : "0.9.1"
       }
     },
     {
@@ -105,17 +132,17 @@
       "kind" : "remoteSourceControl",
       "location" : "https://github.com/StanfordSpezi/SpeziSpeech.git",
       "state" : {
-        "revision" : "0b79f72fc8b0606e09787926446dfafb541669d3",
-        "version" : "1.2.0"
+        "revision" : "3becc70cb1399af9ff954bea22711bb043c517d4",
+        "version" : "1.1.1"
       }
     },
     {
       "identity" : "spezistorage",
       "kind" : "remoteSourceControl",
       "location" : "https://github.com/StanfordSpezi/SpeziStorage.git",
       "state" : {
-        "revision" : "9d04bc622c65002aee704b4de5735970a6e19f46",
-        "version" : "1.1.0"
+        "revision" : "0f4a54430e51f82d29da63a7ce5f61bad7dfb9cd",
+        "version" : "1.2.1"
       }
     },
     {
@@ -127,6 +154,24 @@
         "version" : "1.4.0"
       }
     },
+    {
+      "identity" : "swift-argument-parser",
+      "kind" : "remoteSourceControl",
+      "location" : "https://github.com/apple/swift-argument-parser.git",
+      "state" : {
+        "revision" : "41982a3656a71c768319979febd796c6fd111d5c",
+        "version" : "1.5.0"
+      }
+    },
+    {
+      "identity" : "swift-atomics",
+      "kind" : "remoteSourceControl",
+      "location" : "https://github.com/apple/swift-atomics.git",
+      "state" : {
+        "revision" : "cd142fd2f64be2100422d658e7411e39489da985",
+        "version" : "1.2.0"
+      }
+    },
     {
       "identity" : "swift-collections",
       "kind" : "remoteSourceControl",
@@ -136,6 +181,24 @@
         "version" : "1.1.2"
       }
     },
+    {
+      "identity" : "swift-numerics",
+      "kind" : "remoteSourceControl",
+      "location" : "https://github.com/apple/swift-numerics",
+      "state" : {
+        "revision" : "0a5bc04095a675662cf24757cc0640aa2204253b",
+        "version" : "1.0.2"
+      }
+    },
+    {
+      "identity" : "swift-transformers",
+      "kind" : "remoteSourceControl",
+      "location" : "https://github.com/huggingface/swift-transformers",
+      "state" : {
+        "revision" : "d42fdae473c49ea216671da8caae58e102d28709",
+        "version" : "0.1.14"
+      }
+    },
     {
       "identity" : "xctestextensions",
       "kind" : "remoteSourceControl",

LLMonFHIR.xcodeproj/xcshareddata/xcschemes/LLMonFHIR.xcscheme

@@ -87,7 +87,7 @@
          </CommandLineArgument>
          <CommandLineArgument
             argument = "--testMode"
-            isEnabled = "NO">
+            isEnabled = "YES">
          </CommandLineArgument>
       </CommandLineArguments>
    </LaunchAction>

LLMonFHIR/FHIR Views/FHIRResourcesView.swift

@@ -0,0 +1,145 @@
+//
+// This source file is part of the Stanford Spezi project
+//
+// SPDX-FileCopyrightText: 2023 Stanford University
+//
+// SPDX-License-Identifier: MIT
+//
+
+import SpeziFHIR
+import SwiftUI
+
+
+/// Displays a `List` of all available FHIR resources.
+///
+/// The ``FHIRResourcesView`` displays a SwiftUI `List` of all available resources in the `SpeziFHIR` [`FHIRStore`](https://swiftpackageindex.com/stanfordspezi/spezifhir/documentation/spezifhir/fhirstore).
+/// The FHIR resources are displayed in sections, for example conditions, medications etc.
+/// In order to simply locating a concrete FHIR resource, the ``FHIRResourcesView`` provides a search bar on top of the `List`.
+///
+/// The ``FHIRResourcesView`` contains an optional content as well as action `View` that are located on top of the resource `List` and can be configured via ``FHIRResourcesView/init(navigationTitle:contentView:actionView:)``.
+/// The content and action `View`s are placed within the Swift `List` as a `Section`, enabling proper visual integration with the remainder of the `List`.
+///
+/// - Warning: Ensure that the `SpeziFHIR` [`FHIRStore`](https://swiftpackageindex.com/stanfordspezi/spezifhir/documentation/spezifhir/fhirstore) is properly set up and accessible within the SwiftUI `Environment`.
+///
+/// ### Usage
+///
+/// The example below showcases a minimal example of using the ``FHIRResourcesView``.
+///
+/// ```swift
+/// struct ResourcesView: View {
+///     var body: some View {
+///         FHIRResourcesView(navigationTitle: "...") {
+///             Button("Some Action") {
+///                 // Action to perform
+///                 // ...
+///             }
+///         }
+///     }
+/// }
+/// ```
+public struct FHIRResourcesView<ContentView: View, ActionView: View>: View {
+    @Environment(FHIRStore.self) private var fhirStore
+    @State private var searchText = ""
+
+    private let navigationTitle: Text
+    private let contentView: ContentView
+    private let actionView: ActionView
+
+
+    public var body: some View {
+        List {
+            Section {
+                contentView
+            }
+
+            if searchText.isEmpty {
+                Section {
+                    actionView
+                }
+            }
+
+            if fhirStore.allResources.filterByDisplayName(with: searchText).isEmpty {
+                Text("FHIR_RESOURCES_EMPTY_SEARCH_MESSAGE")
+            } else {
+                resourcesSection
+            }
+
+            Section { } footer: {
+                Text("Total Number of Resources: \(fhirStore.allResources.count)")
+            }
+        }
+            .searchable(text: $searchText)
+            .navigationDestination(for: FHIRResource.self) { resource in
+                InspectResourceView(resource: resource)
+            }
+            .navigationTitle(navigationTitle)
+    }
+
+    @ViewBuilder private var resourcesSection: some View {
+        section(for: \.conditions, sectionName: String(localized: "Conditions"))
+        section(for: \.diagnostics, sectionName: String(localized: "Diagnostics"))
+        section(for: \.encounters, sectionName: String(localized: "Encounters"))
+        section(for: \.immunizations, sectionName: String(localized: "Immunizations"))
+        section(for: \.medications, sectionName: String(localized: "Medications"))
+        section(for: \.observations, sectionName: String(localized: "Observations"))
+        section(for: \.procedures, sectionName: String(localized: "Procedures"))
+        section(for: \.otherResources, sectionName: String(localized: "Other Resources"))
+    }
+
+
+    /// Creates a ``FHIRResourcesView`` displaying a `List` of all available FHIR resources.
+    ///
+    /// - Parameters:
+    ///    - navigationTitle: The localized title displayed for purposes of navigation.
+    ///    - contentView: A custom content `View` that is displayed as the first `Section` of the `List`.
+    ///    - actionView: A custom action `View` that is displayed as the second `Section` of the `List`. Only shown if no search `String` is present.
+    public init(
+        navigationTitle: LocalizedStringResource,
+        @ViewBuilder contentView: () -> ContentView = { EmptyView() },
+        @ViewBuilder _ actionView: () -> ActionView = { EmptyView() }
+    ) {
+        self.navigationTitle = Text(navigationTitle)
+        self.contentView = contentView()
+        self.actionView = actionView()
+    }
+
+    /// Creates a ``FHIRResourcesView`` displaying a `List` of all available FHIR resources.
+    ///
+    /// - Parameters:
+    ///    - navigationTitle: The title displayed for purposes of navigation.
+    ///    - contentView: A custom content `View` that is displayed as the first `Section` of the `List`.
+    ///    - actionView: A custom action `View` that is displayed as the second `Section` of the `List`. Only shown if no search `String` is present.
+    @_disfavoredOverload
+    public init<Title: StringProtocol>(
+        navigationTitle: Title,
+        @ViewBuilder contentView: () -> ContentView = { EmptyView() },
+        @ViewBuilder _ actionView: () -> ActionView = { EmptyView() }
+    ) {
+        self.navigationTitle = Text(verbatim: String(navigationTitle))
+        self.contentView = contentView()
+        self.actionView = actionView()
+    }
+
+
+    private func section(for keyPath: KeyPath<FHIRStore, [FHIRResource]>, sectionName: String) -> some View {
+        var resources = fhirStore[keyPath: keyPath]
+
+        if !searchText.isEmpty {
+            resources = resources.filterByDisplayName(with: searchText)
+        }
+
+        guard !resources.isEmpty else {
+            return AnyView(EmptyView())
+        }
+
+        return AnyView(
+            Section(sectionName) {
+                ForEach(resources) { resource in
+                    NavigationLink(value: resource) {
+                        FHIRResourceSummaryView(resource: resource)
+                    }
+                }
+            }
+        )
+    }
+}