feat(app): improve missing guideline handling

hpi-dhc · Sep 23, 2024 · c98d97f · c98d97f
1 parent 42073f5
commit c98d97f
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Showing 11 changed files with 91 additions and 98 deletions.
diff --git a/app/lib/common/models/drug/cached_drugs.dart b/app/lib/common/models/drug/cached_drugs.dart
@@ -56,17 +56,3 @@ Future<void> initCachedDrugs() async {
   final cachedDrugs = Hive.box<CachedDrugs>(_boxName);
   CachedDrugs._instance = cachedDrugs.get('data') ?? CachedDrugs();
 }
-
-extension CachedDrugsMethods on CachedDrugs {
-  Set<String> get allGuidelineGenes {
-    final guidelineGenes = <String>{};
-    if (CachedDrugs.instance.drugs != null) {
-      for (final drug in CachedDrugs.instance.drugs!) {
-        for (final guideline in drug.guidelines) {
-          guideline.lookupkey.keys.forEach(guidelineGenes.add);
-        }
-      }
-    }
-    return guidelineGenes;
-  }
-}
diff --git a/app/lib/common/models/drug/drug_inhibitors.dart b/app/lib/common/models/drug/drug_inhibitors.dart
@@ -118,7 +118,7 @@ String _getPhenoconversionConsequence(
       ).capitalize()
     : context.l10n.inhibitors_consequence_adapted(
         genotypeResult.geneDisplayString,
-        genotypeResult.phenotype,
+        genotypeResult.phenotypeDisplayString(context),
         displayConfig.userGenitive,
       ).capitalize();
 }
@@ -217,9 +217,9 @@ bool isInhibited(
     genotypeResult.gene,
     drug: drug,
   );
-  final originalPhenotype = genotypeResult.phenotypeDisplayString;
+  final originalPhenotype = genotypeResult.phenotype;
   final phenotypeCanBeInhibited =
-    originalPhenotype.toLowerCase() != overwritePhenotype.toLowerCase();
+    originalPhenotype?.toLowerCase() != overwritePhenotype.toLowerCase();
   return activeInhibitors.isNotEmpty && phenotypeCanBeInhibited;
 }
 
@@ -246,10 +246,11 @@ MapEntry<String, String>? getOverwrittenLookup (
 }
 
 String possiblyAdaptedPhenotype(
+  BuildContext context,
   GenotypeResult genotypeResult,
   { required String? drug }
 ) {
-  final originalPhenotype = genotypeResult.phenotypeDisplayString;
+  final originalPhenotype = genotypeResult.phenotypeDisplayString(context);
   if (!isInhibited(genotypeResult, drug: drug)) {
     return originalPhenotype;
   }

diff --git a/app/lib/common/models/userdata/genotype.dart b/app/lib/common/models/userdata/genotype.dart
@@ -5,5 +5,5 @@ abstract class Genotype{
   });
 
   final String gene;
-  final String variant;
+  final String? variant;
 }
diff --git a/app/lib/common/models/userdata/genotype_key.dart b/app/lib/common/models/userdata/genotype_key.dart
@@ -10,7 +10,7 @@ class GenotypeKey implements Genotype {
   String gene;
 
   @override
-  String variant;
+  String? variant;
 
   bool get isGeneUnique {
     final isDefinedAsNonUnique = definedNonUniqueGenes.contains(gene);
@@ -26,12 +26,21 @@ class GenotypeKey implements Genotype {
   // heavily relies on "non-unique" gene HLA-B, for which the variant is
   // in the format "[allele] [positive/negative]" (which currently is the only)
   // relevant case for "non-unique" genes)
-  String get allele => isGeneUnique ? variant : variant.split(' ').first;
+  String? get allele => variant != null
+    ? isGeneUnique ? variant : variant!.split(' ').first
+    : null;
 
   String get value => isGeneUnique
     ? gene
     : '$gene $allele';
 
   static String extractGene(String genotypeKey) =>
     genotypeKey.split(' ').first;
+
+  static String? maybeExtractVariant(String genotypeKey) {
+    final relevantGenotypeParts = genotypeKey.split(' ');
+    return relevantGenotypeParts.length > 1
+      ? genotypeKey.removePrefix(relevantGenotypeParts.first)
+      : null;
+  }
 }
diff --git a/app/lib/common/models/userdata/genotype_result.dart b/app/lib/common/models/userdata/genotype_result.dart
@@ -1,4 +1,3 @@
-import 'package:collection/collection.dart';
 import 'package:hive/hive.dart';
 
 import '../../module.dart';
@@ -17,29 +16,22 @@ class GenotypeResult implements Genotype {
 
   factory GenotypeResult.fromGenotypeData(
     LabResult labResult,
-    LookupInformation lookup,
+    LookupInformation? lookup,
   ) => GenotypeResult(
     gene: labResult.gene,
     variant: labResult.variant,
     phenotype: labResult.phenotype,
-    lookupkey: lookup.lookupkey,
+    lookupkey: lookup?.lookupkey,
     allelesTested: labResult.allelesTested,
   );
 
-  factory GenotypeResult.missingResult(String gene, BuildContext context) {
-    final potentialLabResultWithoutLookups =
-      UserData.instance.labData?.firstWhereOrNull(
-        (labResult) => labResult.gene == gene
-      );
+  factory GenotypeResult.missingResult(String gene, {String? variant}) {
     return GenotypeResult(
       gene: gene,
-      variant: potentialLabResultWithoutLookups?.variant
-        ?? context.l10n.general_not_tested,
-      phenotype: potentialLabResultWithoutLookups?.phenotype
-        ?? context.l10n.general_not_tested,
-      lookupkey: context.l10n.general_not_tested,
-      allelesTested: potentialLabResultWithoutLookups?.allelesTested
-        ?? context.l10n.general_not_tested,
+      variant: variant,
+      phenotype: null,
+      lookupkey: null,
+      allelesTested: null,
     );
   }
 
@@ -48,39 +40,35 @@ class GenotypeResult implements Genotype {
   String gene;
   @override
   @HiveField(1)
-  String variant;
+  String? variant;
   @HiveField(2)
-  String phenotype;
+  String? phenotype;
   @HiveField(3)
-  String lookupkey;
+  String? lookupkey;
   @HiveField(4)
-  String allelesTested;
+  String? allelesTested;
 
   GenotypeKey get key => GenotypeKey.fromGenotype(this);
 
   String get geneDisplayString => key.value;
 
-  String get variantDisplayString => key.allele;
+  String? get variantDisplayString => key.allele;
 
-  String _removeAllele(String textWithAllele) =>
-    textWithAllele.removePrefix(key.allele).trim().capitalize();
-
-  String get phenotypeDisplayString => key.isGeneUnique
-    ? phenotype
-    : _removeAllele(phenotype);
-  String get genotypeDisplayString => key.isGeneUnique
-    ? variant
-    : _removeAllele(variant);
-}
+  String _removeAlleleOrNull(String textWithAllele) =>
+    key.allele != null
+     ? textWithAllele.removePrefix(key.allele!).trim().capitalize()
+     : textWithAllele;
+
+  String _getDisplayString(BuildContext context, String? text) {
+    final displayString = text ?? context.l10n.general_not_tested;
+    return key.isGeneUnique
+      ? displayString
+      :  _removeAlleleOrNull(displayString);
+  }
 
-extension FindGenotypeResultByKey on Map<String, GenotypeResult> {
-  bool isMissing(String genotypeKey) => this[genotypeKey] == null;
+  String phenotypeDisplayString(BuildContext context) =>
+    _getDisplayString(context, phenotype);
 
-  GenotypeResult findOrMissing(String genotypeKey, BuildContext context) =>
-    isMissing(genotypeKey)
-      ? GenotypeResult.missingResult(
-          GenotypeKey.extractGene(genotypeKey),
-          context,
-        )
-      : this[genotypeKey]!;
+  String genotypeDisplayString(BuildContext context) =>
+    _getDisplayString(context, variant);
 }
diff --git a/app/lib/common/utilities/drug_utils.dart b/app/lib/common/utilities/drug_utils.dart
@@ -22,6 +22,7 @@ Future<void> updateCachedDrugs() async {
   CachedDrugs.instance.drugs = data.drugs;
   CachedDrugs.instance.version = data.version;
   await CachedDrugs.save();
+  await updateGenotypeResults();
   if (previousVersion != null) {
     final context = PharMeApp.navigatorKey.currentContext;
     if (context != null) {

diff --git a/app/lib/common/utilities/genome_data.dart b/app/lib/common/utilities/genome_data.dart
@@ -41,9 +41,35 @@ String formatLookupMapKey(String gene, String variant) {
   return '${gene}__$variant';
 }
 
+Map<String, GenotypeResult> _initializeGenotypeResultKeys() {
+  final emptyGenotypeResults = <String, GenotypeResult>{};
+  for (final drug in CachedDrugs.instance.drugs ?? <Drug>[]) {
+    for (final guideline in drug.guidelines) {
+      for (final gene in guideline.lookupkey.keys) {
+        for (final variant in guideline.lookupkey[gene]!) {
+          final skipLookup = variant == SpecialLookup.anyNotHandled.value ||
+            variant == SpecialLookup.noResult.value;
+          if (skipLookup) continue;
+          final currentGenotypeKey = GenotypeKey(gene, variant);
+          final variantIsRelevant = definedNonUniqueGenes.contains(gene);
+          emptyGenotypeResults[currentGenotypeKey.value] =
+            GenotypeResult.missingResult(
+              gene,
+              variant: variantIsRelevant ? currentGenotypeKey.allele : null,
+            );
+        }
+      }
+    }
+  }
+  return emptyGenotypeResults;
+}
+
 Future<void> updateGenotypeResults() async {
   final skipUpdate = !shouldUpdateGenotypeResults();
   if (skipUpdate) return;
+
+  final genotypeResults = _initializeGenotypeResultKeys();
+
   // fetch lookups
   final response = await get(Uri.parse(cpicLookupUrl));
   if (response.statusCode != 200) throw Exception();
@@ -60,17 +86,14 @@ Future<void> updateGenotypeResults() async {
     lookupsHashMap[variantKey] = lookup;
     if (variantKey != lookupKey) lookupsHashMap[lookupKey] = lookup;
   }
-  final genotypeResults = <String, GenotypeResult>{};
-  // we know that labData is present because we check this in
-  // shouldUpdateGenotypeResults
-  for (final labResult in UserData.instance.labData!) {
+
+  for (final labResult in UserData.instance.labData ?? []) {
     final lookupMapKey = formatLookupMapKey(labResult.gene, labResult.variant);
     final lookup = lookupsHashMap[lookupMapKey];
-    if (lookup == null) continue;
     final genotypeResult = GenotypeResult.fromGenotypeData(labResult, lookup);
+    if (!genotypeResults.keys.contains(genotypeResult.key.value)) continue;
     genotypeResults[genotypeResult.key.value] = genotypeResult;
   }
-
   UserData.instance.genotypeResults = genotypeResults;
   await UserData.save();
 
@@ -80,13 +103,16 @@ Future<void> updateGenotypeResults() async {
 }
 
 bool shouldUpdateGenotypeResults() {
-  final genotypeResultsPresent =
-    UserData.instance.labData?.isNotEmpty ?? false;
+  final genotypeResultsMissing =
+    UserData.instance.genotypeResults?.isEmpty ?? true;
   final lookupsAreOutdated = MetaData.instance.lookupsLastFetchDate == null ||
     DateTime.now().difference(MetaData.instance.lookupsLastFetchDate!) >
       cpicMaxCacheTime;
   final labDataPresent = UserData.instance.labData?.isNotEmpty ?? false;
-  return labDataPresent && (!genotypeResultsPresent || lookupsAreOutdated);
+  final cachedDrugsPresent = CachedDrugs.instance.drugs?.isNotEmpty ?? false;
+  return labDataPresent &&
+    cachedDrugsPresent &&
+    (genotypeResultsMissing || lookupsAreOutdated);
 }
 
 bool shouldFetchDiplotypes() {

diff --git a/app/lib/common/utilities/pdf_utils.dart b/app/lib/common/utilities/pdf_utils.dart
@@ -133,23 +133,17 @@ List<pw.Widget> _buildDrugPart(Drug drug, BuildContext buildContext) {
 }
 
 String? _getPhenotypeInfo(String genotypeKey, Drug drug, BuildContext context) {
-  final genotypeResult = UserData.instance.genotypeResults!.findOrMissing(
-    genotypeKey,
-    context,
-  );
+  final genotypeResult = UserData.instance.genotypeResults![genotypeKey]!;
   if (!isInhibited(genotypeResult, drug: drug.name)) {
-    return genotypeResult.phenotypeDisplayString;
+    return genotypeResult.phenotypeDisplayString(context);
   }
-  return possiblyAdaptedPhenotype(genotypeResult, drug: drug.name);
+  return possiblyAdaptedPhenotype(context, genotypeResult, drug: drug.name);
 }
 
 String? _getPhenoconversionInfo(Drug drug, BuildContext context) {
   if (drug.guidelines.isEmpty) return null;
   final genotypeResults = drug.guidelineGenotypes.map((genotypeKey) =>
-    UserData.instance.genotypeResults!.findOrMissing(
-      genotypeKey,
-      context,
-    )
+    UserData.instance.genotypeResults![genotypeKey]!
   ).toList();
   return '$drugInteractionIndicator ${inhibitionTooltipText(
     context,

diff --git a/app/lib/drug/widgets/annotation_cards/guideline.dart b/app/lib/drug/widgets/annotation_cards/guideline.dart
@@ -117,15 +117,13 @@ class GuidelineAnnotationCard extends StatelessWidget {
       ];
     } else {
       final genotypeResults = drug.guidelineGenotypes.map((genotypeKey) =>
-        UserData.instance.genotypeResults!.findOrMissing(
-          genotypeKey,
-          context,
-        )
+        UserData.instance.genotypeResults![genotypeKey]!
       ).toList();
       final geneDescriptions = genotypeResults.map((genotypeResult) =>
         TableRowDefinition(
           genotypeResult.geneDisplayString,
           possiblyAdaptedPhenotype(
+            context,
             genotypeResult,
             drug: drug.name,
           ),

diff --git a/app/lib/report/pages/gene.dart b/app/lib/report/pages/gene.dart
@@ -55,7 +55,8 @@ class GenePage extends HookWidget {
                             children: [
                               _buildRow(
                                   context.l10n.gene_page_genotype,
-                                  genotypeResult.variantDisplayString,
+                                  genotypeResult.variantDisplayString ??
+                                    context.l10n.general_not_tested,
                                   tooltip: context.l10n.gene_page_genotype_tooltip
                               ),
                               _buildPhenotypeRow(context),
@@ -97,7 +98,7 @@ class GenePage extends HookWidget {
   TableRow _buildPhenotypeRow(BuildContext context) {
     return _buildRow(
       context.l10n.gene_page_phenotype,
-      possiblyAdaptedPhenotype(genotypeResult, drug: null),
+      possiblyAdaptedPhenotype(context, genotypeResult, drug: null),
       tooltip:
         context.l10n.gene_page_phenotype_tooltip,
     );

diff --git a/app/lib/report/pages/report.dart b/app/lib/report/pages/report.dart
@@ -21,18 +21,7 @@ class ReportPage extends StatelessWidget {
   }
 
   Widget _buildReportPage(BuildContext context, ActiveDrugs activeDrugs) {
-    final presentGenes = Set.from(UserData.instance.genotypeResults!.values.map(
-      (genotypeResult) => genotypeResult.gene
-    ));
-    final missingGenes = Set.from(CachedDrugs.instance.allGuidelineGenes.filter(
-      (gene) => !presentGenes.contains(gene)
-    ));
-    final userGenotypes = [
-      ...UserData.instance.genotypeResults!.values,
-      ...missingGenes.map(
-        (gene) => GenotypeResult.missingResult(gene, context),
-      ),
-    ];
+    final userGenotypes = UserData.instance.genotypeResults!.values;
     final warningLevelCounts = <String, WarningLevelCounts>{};
     for (final genotypeResult in userGenotypes) {
       warningLevelCounts[genotypeResult.key.value] = {};
@@ -141,7 +130,7 @@ class GeneCard extends StatelessWidget {
               ),
               SizedBox(height: 8),
               Text(
-                possiblyAdaptedPhenotype(genotypeResult, drug: null),
+                possiblyAdaptedPhenotype(context, genotypeResult, drug: null),
                 style: PharMeTheme.textTheme.titleSmall,
               ),
             ],