Merge pull request #415 from bcgsc/feat/DEVSU-2201-SV-burden-editable

Feat/devsu 2201 sv burden editable

Author: bnguyen-bcgsc

app/components/TumourSummaryEdit/index.tsx

@@ -74,7 +74,10 @@ const TumourSummaryEdit = ({
   useEffect(() => {
     if (mutationBurden) {
       setNewMutationBurdenData({
+        role: mutationBurden.role,
         totalMutationsPerMb: mutationBurden.totalMutationsPerMb,
+        qualitySvCount: mutationBurden.qualitySvCount,
+        qualitySvPercentile: mutationBurden.qualitySvPercentile,
       });
     }
   }, [mutationBurden]);
@@ -339,25 +342,47 @@ const TumourSummaryEdit = ({
     return null;
   }, [handleClicked, handleDelete, handleKeyDown, newMicrobialData]);
 
-  const mutBurDataSection = (
-    <TextField
-      className="tumour-dialog__text-field"
-      label="Mutation Burden (Mut/Mb)"
-      value={newMutationBurdenData?.totalMutationsPerMb ?? 0}
-      name="totalMutationsPerMb"
-      onChange={handleMutationBurdenChange}
-      variant="outlined"
-      fullWidth
-      type="number"
-    />
-  );
+  const mutBurDataSection = useMemo(() => (
+    <>
+      <TextField
+        className="tumour-dialog__text-field"
+        label="Mutation Burden (Mut/Mb)"
+        value={newMutationBurdenData?.totalMutationsPerMb ?? null}
+        name="totalMutationsPerMb"
+        onChange={handleMutationBurdenChange}
+        variant="outlined"
+        fullWidth
+        type="number"
+      />
+      <TextField
+        className="tumour-dialog__text-field"
+        label="SV Burden (POG average)"
+        value={newMutationBurdenData?.qualitySvCount ?? null}
+        name="qualitySvCount"
+        onChange={handleMutationBurdenChange}
+        variant="outlined"
+        fullWidth
+        type="number"
+      />
+      <TextField
+        className="tumour-dialog__text-field"
+        label="SV Burden (Percentile)"
+        value={newMutationBurdenData?.qualitySvPercentile ?? null}
+        name="qualitySvPercentile"
+        onChange={handleMutationBurdenChange}
+        variant="outlined"
+        fullWidth
+        type="number"
+      />
+    </>
+  ), [newMutationBurdenData, handleMutationBurdenChange]);
 
   const tmburMutBurSection = useMemo(() => {
     <>
       <TextField
         className="tumour-dialog__text-field"
         label="genomeSnvTmb"
-        value={newTmburMutData?.genomeSnvTmb ?? 0}
+        value={newTmburMutData?.genomeSnvTmb ?? null}
         name="genomeSnvTmb"
         onChange={handleTmburChange}
         variant="outlined"
@@ -367,7 +392,7 @@ const TumourSummaryEdit = ({
       <TextField
         className="tumour-dialog__text-field"
         label="genomeIndelTmb"
-        value={newTmburMutData?.genomeIndelTmb ?? 0}
+        value={newTmburMutData?.genomeIndelTmb ?? null}
         name="genomeIndelTmb"
         onChange={handleTmburChange}
         variant="outlined"

app/views/ReportView/components/GenomicSummary/index.tsx

@@ -197,6 +197,7 @@ const GenomicSummary = ({
           setVariants(sorted);
           setVariantCounts(counts);
           if (loadedDispatch) {
+            // TODO
             loadedDispatch({ type: 'summary' });
           }
         } catch (err) {

app/views/ReportView/components/RapidSummary/index.tsx

@@ -28,7 +28,7 @@ import './index.scss';
 import TumourSummaryEdit from '@/components/TumourSummaryEdit';
 import DescriptionList from '@/components/DescriptionList';
 import {
-  KbMatchType, TumourSummaryType, ImmuneType, MicrobialType, TmburType,
+  KbMatchType, TumourSummaryType, ImmuneType, MutationBurdenType, MicrobialType, TmburType,
 } from '@/common';
 import useConfirmDialog from '@/hooks/useConfirmDialog';
 import { Box } from '@mui/system';
@@ -147,6 +147,7 @@ const RapidSummary = ({
     value: string | null;
   }[] | null>();
   const [tumourSummary, setTumourSummary] = useState<TumourSummaryType[]>();
+  const [primaryBurden, setPrimaryBurden] = useState<MutationBurdenType>();
   const [tmburMutBur, setTmburMutBur] = useState<TmburType>();
   const [tCellCd8, setTCellCd8] = useState<ImmuneType>();
   const [microbial, setMicrobial] = useState<MicrobialType[]>();
@@ -188,6 +189,18 @@ const RapidSummary = ({
             PromiseSettledResult<MicrobialType[]>,
           ];
 
+          try {
+            const burdenResp = await api.get(`/reports/${report.ident}/mutation-burden`).request();
+            if (burdenResp[0].qualitySvCount == null) {
+              setPrimaryBurden(null);
+            } else {
+              setPrimaryBurden(burdenResp[0]);
+            }
+          } catch (e) {
+            // mutation burden does not exist in records before this implementation, and no backfill will be done on the backend, silent fail this
+            console.error('mutation-burden call error', e?.message);
+          }
+
           if (signaturesResp.status === 'fulfilled') {
             setSignatures(signaturesResp.value);
           } else if (!isPrint) {
@@ -294,6 +307,14 @@ const RapidSummary = ({
     } else {
       msiStatus = null;
     }
+
+    let svBurden: null | string;
+    if (primaryBurden && primaryBurden.qualitySvCount !== null) {
+      svBurden = `${primaryBurden.qualitySvCount} ${primaryBurden.qualitySvPercentile ? `(${primaryBurden.qualitySvPercentile}%)` : ''}`;
+    } else {
+      svBurden = null;
+    }
+
     setTumourSummary([
       {
         term: 'Pathology Tumour Content',
@@ -329,6 +350,10 @@ const RapidSummary = ({
           ? `${tCellCd8.score} ${tCellCd8.percentile ? `(${tCellCd8.percentile}%)` : ''}`
           : null,
       },
+      {
+        term: 'SV Burden (POG Average)',
+        value: svBurden,
+      },
       {
         term: 'Genome TMB (mut/mb)',
         value: tmburMutBur
@@ -340,9 +365,10 @@ const RapidSummary = ({
         value: msiStatus,
       },
     ]);
-  }, [microbial, tmburMutBur, report.m1m2Score, report.sampleInfo, report.tumourContent, tCellCd8?.percentile, tCellCd8?.score, report.captiv8Score]);
+  }, [microbial, primaryBurden, tmburMutBur, report.m1m2Score, report.sampleInfo, report.tumourContent, tCellCd8?.percentile, tCellCd8?.score, report.captiv8Score]);
 
   const handlePatientEditClose = useCallback((
+    // TODO: Argument not being used, leading to OnClose flag on line 744 having too few arguments
     isSaved: boolean,
     newPatientData: PatientInformationType,
     newReportData: ReportType,
@@ -417,12 +443,12 @@ const RapidSummary = ({
     isSaved,
     newMicrobialData,
     newReportData,
-    _mutBurData,
+    newMutationBurdenData: MutationBurdenType,
     newTmBurMutBurData,
   ) => {
     setShowTumourSummaryEdit(false);
 
-    if (!isSaved || (!newMicrobialData && !newReportData && !newTmBurMutBurData)) {
+    if (!isSaved || (!newMicrobialData && !newReportData && !newMutationBurdenData && !newTmBurMutBurData)) {
       return;
     }
 
@@ -434,6 +460,10 @@ const RapidSummary = ({
       setReport(newReportData);
     }
 
+    if (newMutationBurdenData) {
+      setPrimaryBurden(newMutationBurdenData);
+    }
+
     if (newTmBurMutBurData) {
       setTmburMutBur(newTmBurMutBurData);
     }
@@ -454,7 +484,7 @@ const RapidSummary = ({
                 <TumourSummaryEdit
                   microbial={microbial}
                   report={report}
-                  mutationBurden={null}
+                  mutationBurden={primaryBurden}
                   tmburMutBur={tmburMutBur}
                   isOpen={showTumourSummaryEdit}
                   onClose={handleTumourSummaryEditClose}