Merge remote-tracking branch 'origin/main' into adapt-onboarding

.github/workflows/app.yml

@@ -13,7 +13,7 @@ defaults:
 env:
   JAVA_VERSION: 12.x
   FLUTTER_CHANNEL: stable
-  FLUTTER_VERSION: 3.0.3
+  FLUTTER_VERSION: 3.3.4
 
 jobs:
   lint:
@@ -24,7 +24,7 @@ jobs:
       - uses: actions/setup-java@v1
         with:
           java-version: ${{ env.JAVA_VERSION }}
-      - uses: subosito/flutter-action@v1
+      - uses: subosito/flutter-action@v2
         with:
           channel: ${{ env.FLUTTER_CHANNEL }}
           flutter-version: ${{ env.FLUTTER_VERSION }}

anni/src/components/bricks/BrickForm.tsx

@@ -85,6 +85,7 @@ const BrickForm = ({ usage, brick }: Props) => {
             setMessage(`Failed to ${id ? 'update' : 'add new'} Brick.`);
         }
     };
+    // eslint-disable-next-line @typescript-eslint/no-unused-vars
     const deleteBrick = async () => {
         try {
             await axios.delete(`/api/bricks/${id}`);
@@ -144,7 +145,9 @@ const BrickForm = ({ usage, brick }: Props) => {
                     Cancel
                 </WithIcon>
                 <div className="space-x-4">
-                    {id && (
+                    {/*
+                    // Disabled for #378 until proper handling of deletion
+                    id && (
                         <WithIcon
                             as="button"
                             icon={TrashIcon}
@@ -153,7 +156,7 @@ const BrickForm = ({ usage, brick }: Props) => {
                         >
                             Delete Brick
                         </WithIcon>
-                    )}
+                    )*/}
                     <WithIcon
                         as="button"
                         icon={UploadIcon}

app/integration_test/drugs_test.dart

@@ -50,7 +50,15 @@ void main() {
         geneSymbol: 'CYP2C9',
         phenotype: 'Normal Metabolizer',
         genotype: '*1/*1',
-        lookupkey: 'Normal Metabolizer')
+        lookupkey: '2')
+  };
+  UserData.instance.diplotypes = {
+    'CYP2C9': Diplotype(
+        gene: 'CYP2C9',
+        resultType: 'Diplotype',
+        phenotype: 'Normal Metabolizer',
+        genotype: '*1/*1',
+        allelesTested: '1')
   };
   final testDrugWithoutGuidelines = Drug(
     id: '2',
@@ -63,7 +71,7 @@ void main() {
         brandNames: ['brand name', 'another brand name']),
     guidelines: [],
   );
-  UserData.instance.starredDrugIds = ['1'];
+  UserData.instance.activeDrugNames = ['Ibuprofen'];
 
   group('integration test for the drugs page', () {
     testWidgets('test loading', (tester) async {
@@ -116,7 +124,7 @@ void main() {
 
     testWidgets('test loaded page', (tester) async {
       when(() => mockDrugsCubit.state)
-          .thenReturn(DrugState.loaded(testDrug, isStarred: false));
+          .thenReturn(DrugState.loaded(testDrug, isActive: false));
 
       late BuildContext context;
 
@@ -180,7 +188,7 @@ void main() {
 
     testWidgets('test loaded page without guidelines', (tester) async {
       when(() => mockDrugsCubit.state).thenReturn(
-          DrugState.loaded(testDrugWithoutGuidelines, isStarred: true));
+          DrugState.loaded(testDrugWithoutGuidelines, isActive: true));
 
       await tester.pumpWidget(
         MaterialApp(

app/integration_test/search_test.dart

@@ -8,7 +8,7 @@ import 'package:mocktail/mocktail.dart';
 
 class MockSearchCubit extends MockCubit<SearchState> implements SearchCubit {
   @override
-  bool get filterStarred => false;
+  FilterState get filter => FilterState.initial();
 }
 
 void main() {
@@ -71,7 +71,7 @@ void main() {
 
     testWidgets('test search page in loaded state', (tester) async {
       when(() => mockSearchCubit.state)
-          .thenReturn(SearchState.loaded(loadedDrugs, loadedDrugs));
+          .thenReturn(SearchState.loaded(loadedDrugs, FilterState.initial()));
 
       await tester.pumpWidget(BlocProvider.value(
         value: mockSearchCubit,

app/integration_test/settings_test.dart

@@ -44,7 +44,7 @@ void main() {
       );
 
       // close dialog
-      await tester.tap(find.text(context.l10n.settings_page_cancel));
+      await tester.tap(find.text(context.l10n.action_cancel));
       await tester.pumpAndSettle();
 
       // test onboarding button

app/lib/common/models/drug/drug.dart

@@ -66,9 +66,9 @@ class DrugAnnotations {
   List<String> brandNames;
 }
 
-extension DrugIsStarred on Drug {
-  bool isStarred() {
-    return UserData.instance.starredDrugIds?.contains(id) ?? false;
+extension DrugIsActive on Drug {
+  bool isActive() {
+    return UserData.instance.activeDrugNames?.contains(name) ?? false;
   }
 }
 
@@ -80,52 +80,20 @@ extension DrugMatchesQuery on Drug {
   }
 }
 
-/// Removes the guidelines that are not relevant to the user
-extension DrugWithUserGuidelines on Drug {
-  Drug filterUserGuidelines() {
-    final matchingGuidelines = guidelines.where((guideline) {
-      // Guideline matches if all user has any of the gene results for all gene
-      // symbols
-      return guideline.lookupkey.all((geneSymbol, geneResults) =>
-          (UserData.instance.lookups?.containsKey(geneSymbol) ?? false) &&
-          geneResults
-              .contains(UserData.instance.lookups?[geneSymbol]?.lookupkey));
-    });
-
-    return Drug(
-      id: id,
-      version: version,
-      name: name,
-      rxNorm: rxNorm,
-      annotations: annotations,
-      guidelines: matchingGuidelines.toList(),
-    );
-  }
-}
-
-/// Removes the guidelines that are not relevant to the user
-extension DrugsWithUserGuidelines on List<Drug> {
-  List<Drug> filterUserGuidelines() {
-    return map((drug) => drug.filterUserGuidelines()).toList();
-  }
+/// Gets the User's matching guideline
+extension DrugWithUserGuideline on Drug {
+  Guideline? userGuideline() => guidelines.firstOrNullWhere(
+        (guideline) => guideline.lookupkey.all((geneSymbol, geneResults) =>
+            geneResults.contains(UserData.lookupFor(geneSymbol))),
+      );
 }
 
 /// Filters for drugs with non-OK warning level
 extension CriticalDrugs on List<Drug> {
   List<Drug> filterCritical() {
     return filter((drug) {
-      final warningLevel = drug.highestWarningLevel();
+      final warningLevel = drug.userGuideline()?.annotations.warningLevel;
       return warningLevel != null && warningLevel != WarningLevel.green;
     }).toList();
   }
 }
-
-/// Gets most severe warning level
-extension DrugWarningLevel on Drug {
-  WarningLevel? highestWarningLevel() {
-    final filtered = filterUserGuidelines();
-    return filtered.guidelines
-        .map((guideline) => guideline.annotations.warningLevel)
-        .maxBy((level) => level.severity);
-  }
-}

app/lib/common/models/drug/drug_inhibitors.dart

@@ -0,0 +1,24 @@
+// Everything has to match literally. The final value is not a phenotype but
+// the CPIC lookupkey value. If a user has multiple of the given drugs active,
+// the topmost one will be used, i.e. the inhibitors should go from most to
+// least severe.
+
+// structure: gene symbol -> drug name -> overwriting lookupkey
+
+const Map<String, Map<String, String>> drugInhibitors = {
+  'CYP2D6': {
+    // 0.0 is a lookupkey for a type of poor metabolizer
+    'bupropion': '0.0',
+    'fluoxetine': '0.0',
+    'paroxetine': '0.0',
+    'quinidine': '0.0',
+    'terbinafine': '0.0',
+    // 1.0 is a lookupkey for a type of poor (but less poor than 0.0)
+    // metabolizer
+    'abiraterone': '1.0',
+    'cinacalcet': '1.0',
+    'duloxetine': '1.0',
+    'lorcaserin': '1.0',
+    'mirabegron': '1.0',
+  }
+};

app/lib/common/models/drug/warning_level.dart

@@ -10,7 +10,9 @@ enum WarningLevel {
   @HiveField(1)
   yellow,
   @HiveField(2)
-  green
+  green,
+  @HiveField(3)
+  none,
 }
 
 extension WarningLevelIcon on WarningLevel {

app/lib/common/models/module.dart

@@ -1,5 +1,6 @@
 export 'anni_response.dart';
 export 'drug/drug.dart';
+export 'drug/drug_inhibitors.dart';
 export 'drug/guideline.dart';
 export 'drug/warning_level.dart';
 export 'metadata.dart';

app/lib/common/models/userdata/userdata.dart

@@ -1,3 +1,4 @@
+import 'package:collection/collection.dart';
 import 'package:hive/hive.dart';
 
 import '../../../search/module.dart';
@@ -30,13 +31,33 @@ class UserData {
   }
 
   @HiveField(0)
-  List<Diplotype>? diplotypes;
+  Map<String, Diplotype>? diplotypes;
+  static String? phenotypeFor(String gene) =>
+      UserData.instance.diplotypes?[gene]?.phenotype;
 
   @HiveField(1)
   Map<String, CpicPhenotype>? lookups;
 
+  static MapEntry<String, String>? overwrittenLookup(String gene) {
+    final inhibitors = drugInhibitors[gene];
+    if (inhibitors == null) return null;
+    final lookup = inhibitors.entries.firstWhereOrNull((entry) =>
+        UserData.instance.activeDrugNames?.contains(entry.key) ?? false);
+    if (lookup == null) return null;
+    return lookup;
+  }
+
+  static String? lookupFor(String gene) {
+    final overwrittenLookup = UserData.overwrittenLookup(gene);
+    if (overwrittenLookup != null) {
+      return overwrittenLookup.value;
+    }
+    return UserData.instance.lookups?[gene]?.lookupkey;
+  }
+
+  // hive can't deal with sets so we have to use a list :(
   @HiveField(2)
-  List<String>? starredDrugIds;
+  List<String>? activeDrugNames;
 }
 
 /// Initializes the user's data by registering all necessary adapters and

app/lib/common/pages/drug/cubit.dart

@@ -6,32 +6,34 @@ part 'cubit.freezed.dart';
 
 class DrugCubit extends Cubit<DrugState> {
   DrugCubit(this._drug) : super(DrugState.initial()) {
-    emit(DrugState.loaded(_drug, isStarred: _drug.isStarred()));
+    emit(DrugState.loaded(_drug, isActive: _drug.isActive()));
   }
 
   final Drug _drug;
 
-  Future<void> toggleStarred() async {
+  // ignore: avoid_positional_boolean_parameters
+  Future<void> setActivity(bool? value) async {
+    if (value == null) return;
     final drug = state.whenOrNull(loaded: (drug, _) => drug);
     if (drug == null) return;
 
-    final stars = UserData.instance.starredDrugIds ?? [];
-    if (drug.isStarred()) {
-      UserData.instance.starredDrugIds =
-          stars.filter((element) => element != _drug.id).toList();
-    } else {
-      UserData.instance.starredDrugIds = stars + [_drug.id];
+    final active = (UserData.instance.activeDrugNames ?? [])
+        .filter((name) => name != _drug.name)
+        .toList();
+    if (value) {
+      active.add(_drug.name);
     }
+    UserData.instance.activeDrugNames = active;
     await UserData.save();
-    emit(DrugState.loaded(drug, isStarred: drug.isStarred()));
+    emit(DrugState.loaded(drug, isActive: value));
   }
 }
 
 @freezed
 class DrugState with _$DrugState {
   const factory DrugState.initial() = _InitialState;
   const factory DrugState.loading() = _LoadingState;
-  const factory DrugState.loaded(Drug drug, {required bool isStarred}) =
+  const factory DrugState.loaded(Drug drug, {required bool isActive}) =
       _LoadedState;
   const factory DrugState.error() = _ErrorState;
 }

app/lib/common/pages/drug/drug.dart

@@ -28,13 +28,9 @@ class DrugPage extends StatelessWidget {
                 body: [errorIndicator(context.l10n.err_generic)]),
             loading: () =>
                 pageScaffold(title: drugName, body: [loadingIndicator()]),
-            loaded: (drug, isStarred) => pageScaffold(
+            loaded: (drug, isActive) => pageScaffold(
               title: drugName,
               actions: [
-                IconButton(
-                  onPressed: () => context.read<DrugCubit>().toggleStarred(),
-                  icon: PharMeTheme.starIcon(isStarred: isStarred),
-                ),
                 IconButton(
                   onPressed: () => sharePdf(drug),
                   icon: Icon(
@@ -44,7 +40,7 @@ class DrugPage extends StatelessWidget {
                 )
               ],
               body: [
-                _buildDrugsPage(drug, isStarred: isStarred, context: context)
+                _buildDrugsPage(drug, isActive: isActive, context: context)
               ],
             ),
           );
@@ -55,28 +51,33 @@ class DrugPage extends StatelessWidget {
 
   Widget _buildDrugsPage(
     Drug drug, {
-    required bool isStarred,
+    required bool isActive,
     required BuildContext context,
   }) {
+    final userGuideline = drug.userGuideline();
     return Padding(
         padding: const EdgeInsets.symmetric(horizontal: 12, vertical: 16),
         child: Column(
           crossAxisAlignment: CrossAxisAlignment.start,
           children: [
-            SubHeader(context.l10n.drugs_page_header_druginfo),
+            SubHeader(context.l10n.drugs_page_header_drug),
             SizedBox(height: 12),
-            DrugAnnotationCard(drug),
+            DrugAnnotationCard(
+              drug,
+              isActive: isActive,
+              setActivity: context.read<DrugCubit>().setActivity,
+            ),
             SizedBox(height: 20),
             SubHeader(
               context.l10n.drugs_page_header_guideline,
               tooltip: context.l10n.drugs_page_tooltip_guideline,
             ),
             SizedBox(height: 12),
-            ...(drug.guidelines.isNotEmpty)
+            ...(userGuideline != null)
                 ? [
                     Disclaimer(),
                     SizedBox(height: 12),
-                    GuidelineAnnotationCard(drug.guidelines[0])
+                    GuidelineAnnotationCard(userGuideline)
                   ]
                 : [Text(context.l10n.drugs_page_no_guidelines_for_phenotype)]
           ],