feat(#684): introduce GenotypeResult

hpi-dhc · Feb 12, 2024 · d709260 · d709260
1 parent 483c3f1
commit d709260
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Showing 21 changed files with 280 additions and 214 deletions.
diff --git a/app/generate_screenshots/app_test.dart b/app/generate_screenshots/app_test.dart
@@ -34,7 +34,7 @@ void main() {
 
       // Part before runApp in lib/main.dart
       await initServices();
-      await fetchAndSaveLookups();
+      await updateGenotypeResults();
 
       // Load the app
       await tester.pumpWidget(

diff --git a/app/integration_test/drugs_test.dart b/app/integration_test/drugs_test.dart
@@ -19,49 +19,52 @@ void main() {
   binding.framePolicy = LiveTestWidgetsFlutterBindingFramePolicy.onlyPumps;
 
   final testDrug = Drug(
-      id: '1',
-      version: 1,
-      name: 'Ibuprofen',
-      rxNorm: 'rxnorm',
-      annotations: DrugAnnotations(
-          drugclass: 'NSAID',
-          indication: 'indication',
-          brandNames: ['brand name', 'another brand name']),
-      guidelines: [
-        Guideline(
-            id: '1',
-            version: 1,
-            lookupkey: {
-              'CYP2C9': ['2']
-            },
-            externalData: [
-              GuidelineExtData(
-                  source: 'CPIC',
-                  guidelineName: 'cpic name',
-                  guidelineUrl: 'cpic url',
-                  implications: {'CYP2C9': 'normal metabolization'},
-                  recommendation: 'default dose',
-                  comments: 'comments')
-            ],
-            annotations: GuidelineAnnotations(
+    id: '1',
+    version: 1,
+    name: 'Ibuprofen',
+    rxNorm: 'rxnorm',
+    annotations: DrugAnnotations(
+        drugclass: 'NSAID',
+        indication: 'indication',
+        brandNames: ['brand name', 'another brand name']),
+    guidelines: [
+      Guideline(
+          id: '1',
+          version: 1,
+          lookupkey: {
+            'CYP2C9': ['2']
+          },
+          externalData: [
+            GuidelineExtData(
+                source: 'CPIC',
+                guidelineName: 'cpic name',
+                guidelineUrl: 'cpic url',
+                implications: {'CYP2C9': 'normal metabolization'},
                 recommendation: 'default dose',
-                implication: 'nothing',
-                warningLevel: WarningLevel.green))
-      ]);
-  UserData.instance.lookups = {
-    'CYP2C9': LookupInformation(
-        gene: 'CYP2C9',
-        phenotype: 'Normal Metabolizer',
-        variant: '*1/*1',
-        lookupkey: '2')
-  };
-  UserData.instance.geneResults = {
-    'CYP2C9': GeneResult(
+                comments: 'comments')
+          ],
+          annotations: GuidelineAnnotations(
+              recommendation: 'default dose',
+              implication: 'nothing',
+              warningLevel: WarningLevel.green))
+    ]);
+    UserData.instance.geneResults = [
+      GeneResult(
         gene: 'CYP2C9',
         phenotype: 'Normal Metabolizer',
         variant: '*1/*1',
-        allelesTested: '1')
-  };
+        allelesTested: '1',
+      ),
+    ];
+    UserData.instance.genotypeResults = {
+      'CYP2C9': GenotypeResult(
+        gene: UserData.instance.geneResults![0].gene,
+        phenotype: UserData.instance.geneResults![0].phenotype,
+        variant: UserData.instance.geneResults![0].variant,
+        allelesTested: UserData.instance.geneResults![0].variant,
+        lookupkey: '2',
+      ),
+    };
   final testDrugWithoutGuidelines = Drug(
     id: '2',
     version: 1,

diff --git a/app/integration_test/main_page_test.dart b/app/integration_test/main_page_test.dart
@@ -9,7 +9,7 @@ void main() {
 
   binding.framePolicy = LiveTestWidgetsFlutterBindingFramePolicy.onlyPumps;
 
-  UserData.instance.lookups = {};
+  UserData.instance.genotypeResults = {};
 
   CachedDrugs.instance.version = 1;
   CachedDrugs.instance.drugs = List.empty();

diff --git a/app/lib/common/models/drug/drug.dart b/app/lib/common/models/drug/drug.dart
@@ -88,8 +88,12 @@ extension DrugExtension on Drug {
   Guideline? get userOrFirstGuideline => userGuideline ??
     (guidelines.isNotEmpty ? guidelines.first : null);
 
-  List<String> get guidelineGenes => guidelines.isNotEmpty
-    ? guidelines.first.lookupkey.keys.toList()
+  List<String> get guidelineGenotypes => guidelines.isNotEmpty
+    ? guidelines.first.lookupkey.keys.flatMap(
+      (gene) => guidelines.first.lookupkey[gene]!.map((variant) =>
+        GenotypeKey(gene, variant).value
+      ).toList()
+    ).toList()
     : [];
 
   WarningLevel get warningLevel =>

diff --git a/app/lib/common/models/drug/drug_inhibitors.dart b/app/lib/common/models/drug/drug_inhibitors.dart
@@ -83,7 +83,7 @@ List<String> inhibitorsFor(String gene) {
   return _drugInhibitorsPerGene[gene] ?? [];
 }
 
-bool canBeInhibited(LookupInformation lookup) {
-  return inhibitableGenes.contains(lookup.gene) &&
-    lookup.lookupkey != '0.0';
+bool canBeInhibited(GenotypeResult genotypeResult) {
+  return inhibitableGenes.contains(genotypeResult.gene) &&
+    genotypeResult.lookupkey != '0.0';
 }
diff --git a/app/lib/common/models/module.dart b/app/lib/common/models/module.dart
@@ -7,5 +7,8 @@ export 'drug/warning_level.dart';
 export 'metadata.dart';
 export 'userdata/gene_result.dart';
 export 'userdata/genotype.dart';
+export 'userdata/genotype_key.dart';
+export 'userdata/genotype_result.dart';
 export 'userdata/lookup_information.dart';
+export 'userdata/phenotype_information.dart';
 export 'userdata/userdata.dart';
diff --git a/app/lib/common/models/userdata/genotype.dart b/app/lib/common/models/userdata/genotype.dart
@@ -1,9 +1,9 @@
 abstract class Genotype{
-  Genotype({
+  const Genotype({
     required this.gene,
     required this.variant,
   });
 
-  String gene;
-  String variant;
+  final String gene;
+  final String variant;
 }
diff --git a/app/lib/common/models/userdata/genotype_key.dart b/app/lib/common/models/userdata/genotype_key.dart
@@ -0,0 +1,27 @@
+import '../../module.dart';
+
+class GenotypeKey implements Genotype {
+  GenotypeKey(this.gene, this.variant);
+
+  factory GenotypeKey.fromGenotype(Genotype genotype) =>
+    GenotypeKey(genotype.gene, genotype.variant);
+
+  @override
+  String gene;
+
+  @override
+  String variant;
+
+  String get value {
+    final geneResults = UserData.instance.geneResults!.where(
+    (geneResult) => geneResult.gene == gene
+    );
+    if (geneResults.length > 1) {
+      return '$gene ${variant.split(' ').first}';
+    }
+    return gene;
+  }
+
+  static String extractGene(String genotypeKey) =>
+    genotypeKey.split(' ').first;
+}
diff --git a/app/lib/common/models/userdata/genotype_result.dart b/app/lib/common/models/userdata/genotype_result.dart
@@ -0,0 +1,59 @@
+import 'package:hive/hive.dart';
+
+import '../../module.dart';
+
+part 'genotype_result.g.dart';
+
+@HiveType(typeId: 2)
+class GenotypeResult implements Genotype {
+  GenotypeResult({
+    required this.gene,
+    required this.variant,
+    required this.phenotype,
+    required this.lookupkey,
+    required this.allelesTested,
+  });
+
+  factory GenotypeResult.fromGenotypeData(
+    GeneResult labResult,
+    LookupInformation lookup,
+  ) => GenotypeResult(
+    gene: labResult.gene,
+    variant: labResult.variant,
+    phenotype: labResult.phenotype,
+    lookupkey: lookup.lookupkey,
+    allelesTested: labResult.allelesTested,
+  );
+
+  factory GenotypeResult.missingResult(String gene, BuildContext context) =>
+    GenotypeResult(
+      gene: gene,
+      variant: context.l10n.general_not_tested,
+      phenotype: context.l10n.general_not_tested,
+      lookupkey: context.l10n.general_not_tested,
+      allelesTested: context.l10n.general_not_tested,
+    );
+
+  @override
+  @HiveField(0)
+  String gene;
+  @override
+  @HiveField(1)
+  String variant;
+  @HiveField(2)
+  String phenotype;
+  @HiveField(3)
+  String lookupkey;
+  @HiveField(4)
+  String allelesTested;
+
+  String get key => GenotypeKey.fromGenotype(this).value;
+}
+
+extension FindGenotypeResultByKey on Map<String, GenotypeResult> {
+  GenotypeResult findOrMissing(String genotypeKey, BuildContext context) =>
+    this[genotypeKey] ?? GenotypeResult.missingResult(
+      GenotypeKey.extractGene(genotypeKey),
+      context,
+    );
+}
diff --git a/app/lib/common/models/userdata/lookup_information.dart b/app/lib/common/models/userdata/lookup_information.dart
@@ -1,12 +1,5 @@
-import 'package:freezed_annotation/freezed_annotation.dart';
-import 'package:hive/hive.dart';
-
 import 'genotype.dart';
 
-part 'lookup_information.g.dart';
-
-@HiveType(typeId: 2)
-@JsonSerializable()
 class LookupInformation implements Genotype {
   LookupInformation({
     required this.gene,
@@ -16,28 +9,18 @@ class LookupInformation implements Genotype {
   });
 
   factory LookupInformation.fromJson(dynamic json) {
-    return _$LookupInformationFromJson({
-      ...json,
-      // transform lookupkey map to string
-      'lookupkey': json['lookupkey'][json['genesymbol']],
-    });
+    return LookupInformation(
+        gene: json['genesymbol'] as String,
+        variant: json['diplotype'] as String,
+        phenotype: json['generesult'] as String,
+        lookupkey: json['lookupkey'][json['genesymbol']] as String,
+    );
   }
 
   @override
-  @HiveField(0)
-  @JsonKey(name: 'genesymbol')
   String gene;
-
   @override
-  @HiveField(1)
-  @JsonKey(name: 'diplotype')
   String variant;
-
-  @HiveField(2)
-  @JsonKey(name: 'generesult')
   String phenotype;
-
-  @HiveField(3)
-  @JsonKey(name: 'lookupkey')
   String lookupkey;
 }
diff --git a/app/lib/common/models/userdata/phenotype_information.dart b/app/lib/common/models/userdata/phenotype_information.dart
@@ -0,0 +1,11 @@
+class PhenotypeInformation {
+  PhenotypeInformation({
+    required this.phenotype,
+    this.adaptionText,
+    this.overwrittenPhenotypeText,
+  });
+
+  String phenotype;
+  String? adaptionText;
+  String? overwrittenPhenotypeText;
+}