Merge pull request #254 from bcgsc/bugfix/DEVSU-1996-fix-tmb-filtering

bugfix/DEVSU-1996-fix-tmb-filtering
bcgsc · May 15, 2023 · 6234439 · 6234439
2 parents ce72a67 + 895ca12
commit 6234439
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Showing 2 changed files with 17 additions and 4 deletions.
diff --git a/app/routes/report/variants.js b/app/routes/report/variants.js
@@ -59,14 +59,13 @@ const cancerRelevanceFilter = {
   },
   variantType: {[Op.and]: [
     {[Op.is]: literal('distinct from \'exp\'')},
-    {[Op.is]: literal('distinct from \'tmb\'')},
   ]},
   // Regex filter for finding columns with 2 or more spaces that end with
   // mutation or mutations
   [Op.not]: {kbVariant: {[Op.regexp]: MUTATION_REGEX}},
 };
 
-const unknownSignificanceIncludes = ['mut', 'tmb'];
+const unknownSignificanceIncludes = ['mut'];
 const signatureVariant = ['tmb', 'msi'];
 
 const unknownSignificanceGeneFilter = {

diff --git a/test/routes/report/variants.test.js b/test/routes/report/variants.test.js
@@ -112,6 +112,7 @@ describe('/reports/{REPORTID}/kb-matches', () => {
   let rapidDataIprB;
   let rapidDataAlreadyReported;
   let rapidDataIprANotTherapeuticMsi;
+  let rapidDataIprANotTherapeuticTmb;
   let rapidDataIprANotTherapeutic;
   let rapidDataTherapeuticIprC;
   let rapidDataTherapeuticIprCGeneric;
@@ -126,6 +127,7 @@ describe('/reports/{REPORTID}/kb-matches', () => {
   let kbMatchRapidDataIprB;
   let kbMatchRapidDataIprANotTherapeutic;
   let kbMatchRapidDataIprANotTherapeuticMsi;
+  let kbMatchRapidDataIprANotTherapeuticTmb;
   let kbMatchRapidDataAlreadyReported;
   let kbMatchRapidDataTherapeuticIprC;
   let kbMatchRapidDataTherapeuticIprCGeneric;
@@ -245,7 +247,6 @@ describe('/reports/{REPORTID}/kb-matches', () => {
     });
     rapidVariantTmb = await db.models.tmburMutationBurden.create({
       reportId: rapidReport.id,
-      geneId: rapidGeneUSAllTrue.id,
     });
 
     rapidDataIprA = {
@@ -295,6 +296,15 @@ describe('/reports/{REPORTID}/kb-matches', () => {
       kbVariant: 'also should be table 2',
     };
 
+    rapidDataIprANotTherapeuticTmb = {
+      reportId: rapidReport.id,
+      variantId: rapidVariantTmb.id,
+      category: 'unknown',
+      variantType: 'tmb',
+      iprEvidenceLevel: 'IPR-A',
+      kbVariant: 'geneX specific mutation',
+    };
+
     rapidDataTherapeuticIprC = {
       reportId: rapidReport.id,
       variantId: rapidVariantCR.id,
@@ -378,6 +388,9 @@ describe('/reports/{REPORTID}/kb-matches', () => {
     kbMatchRapidDataIprANotTherapeuticMsi = await db.models.kbMatches.create(
       rapidDataIprANotTherapeuticMsi,
     );
+    kbMatchRapidDataIprANotTherapeuticTmb = await db.models.kbMatches.create(
+      rapidDataIprANotTherapeuticTmb,
+    );
     kbMatchRapidDataAlreadyReported = await db.models.kbMatches.create(
       rapidDataAlreadyReported,
     );
@@ -410,6 +423,7 @@ describe('/reports/{REPORTID}/kb-matches', () => {
       kbMatchRapidDataIprUnknownNull,
       kbMatchRapidDataIprAMatchedCancerFalse,
       kbMatchRapidDataIprANotTherapeuticMsi,
+      kbMatchRapidDataIprANotTherapeuticTmb,
     ];
     unknownSignificanceMatches = [
       kbMatchRapidDataIprAGeneric,
@@ -426,12 +440,12 @@ describe('/reports/{REPORTID}/kb-matches', () => {
     cancerRelevanceVariants = [
       rapidVariantCR,
       rapidVariantMsi,
+      rapidVariantTmb,
     ];
     unknownSignificanceVariants = [
       rapidVariantUSOncogene,
       rapidVariantUStumourSuppressor,
       rapidVariantUSAllTrue,
-      rapidVariantTmb,
       rapidVariantTAGeneric,
       rapidVariantCRGeneric,
     ];