DEVSU-3003 Do not display variant in TGR moves to VUS

app/routes/report/variants.js

@@ -116,12 +116,18 @@ const getRapidReportVariants = async (tableName, variantType, reportId, rapidTab
   const unknownSignificanceFromAnnotation = [];
   const unknownSignificanceFromGeneProperty = [];
   const doNotReport = [];
+  const doNotReportIdents = new Set();
 
   const tumourSuppressorLofVariants = {};
 
   // separate out variants that qualify based on gene properties alone, if filtering for table 3
   if (rapidTable === 'unknownSignificance') {
     for (const variant of allKbMatches) {
+      if (variant?.observedVariantAnnotation?.annotations?.rapidReportTableTag === 'noTable') {
+        doNotReport.push(variant);
+        doNotReportIdents.add(variant.ident);
+        continue;
+      }
       if (variant.gene.cancerGeneListMatch
           || variant.gene.oncogene
           || variant.gene.tumourSuppressor) {
@@ -180,7 +186,9 @@ const getRapidReportVariants = async (tableName, variantType, reportId, rapidTab
         } else if (tableTag === 'unknownSignificance') {
           unknownSignificanceFromAnnotation.push(variant);
         } else if (tableTag === 'noTable') {
+          console.log(`Variant ${variant.ident} is tagged as noTable, will not be reported`);
           doNotReport.push(variant);
+          doNotReportIdents.add(variant.ident);
         }
       }
     }
@@ -356,7 +364,7 @@ const getRapidReportVariants = async (tableName, variantType, reportId, rapidTab
   const existingVariants = new Set(unknownSignificanceResults.map((variant) => {return variant.ident;}));
 
   unknownSignificanceFromGeneProperty.forEach((variant) => {
-    if (!existingVariants.has(variant.ident)) {
+    if (!existingVariants.has(variant.ident) && !doNotReportIdents.has(variant.ident)) {
       unknownSignificanceResults.push(variant);
       existingVariants.add(variant.ident);
     }
@@ -377,7 +385,9 @@ const getRapidReportVariants = async (tableName, variantType, reportId, rapidTab
   // reason there may be to exclude them
   unknownSignificanceResultsFiltered.push(...unknownSignificanceFromAnnotation);
 
-  return unknownSignificanceResultsFiltered;
+  return unknownSignificanceResultsFiltered.filter((variant) => {
+    return !doNotReportIdents.has(variant.ident);
+  });
 };
 
 const updateKbDataSummaryTableTag = (kbData, rapidTable, variantType, variantIdent) => {

test/routes/report/variants.test.js

@@ -904,6 +904,39 @@ describe('/reports/{REPORTID}/variants', () => {
       await db.models.report.destroy({where: {ident: reportIdent.ident}});
     });
 
+    test('Variants tagged noTable stay out of table 3 even when gene properties qualify and there are no kbmatches - OK', async () => {
+      const newMockReportData = JSON.parse(JSON.stringify(mockReportData));
+      newMockReportData.genes = newMockReportData.genes.concat([
+        {name: 'TA5gene', oncogene: true},
+      ]);
+      newMockReportData.smallMutations = newMockReportData.smallMutations.concat([{
+        gene: 'TA5gene',
+        key: 'TA5',
+        displayName: 'TA5',
+      }]);
+
+      const reportIdent = await createReport(newMockReportData);
+
+      const ta5Variant = await db.models.smallMutations.findOne({
+        where: {
+          reportId: reportIdent.id,
+          displayName: 'TA5',
+        },
+      });
+
+      await db.models.observedVariantAnnotations.create({
+        variantId: ta5Variant.id,
+        variantType: 'mut',
+        annotations: {rapidReportTableTag: 'noTable'},
+        reportId: reportIdent.id,
+      });
+
+      const table = await checkRapidReportTable(reportIdent.ident, 'TA5', 'mut');
+      expect(table).toBe('noTable');
+
+      await db.models.report.destroy({where: {ident: reportIdent.ident}});
+    });
+
     test('LOF promotion: Qualifying mutation-type matches promoted if lof variant on tumour suppressor gene found - OK', async () => {
       // TA1 - expect lof promotion to occur - table 1
       const newMockReportData = JSON.parse(JSON.stringify(mockReportData));