Feat: Add Editable Fields For Tumour Summary

- DEVSU-2201
- Add editable tumour summary fields (role, mutation burden mut/mb, sv count, sv percentile) in both Genomic and Rapid reports
- Flag some errors (code as TODO)

Author: bnguyen-bcgsc

app/components/TumourSummaryEdit/index.scss

@@ -6,4 +6,8 @@
   &__text-field {
     margin: 12px 0;
   }
+
+  &__drop-down {
+    margin: 12px 0;
+  }
 }

app/components/TumourSummaryEdit/index.tsx

@@ -10,6 +10,8 @@ import {
   Button,
   Chip,
   Autocomplete,
+  Select,
+  MenuItem,
 } from '@mui/material';
 import cloneDeep from 'lodash/cloneDeep';
 import api, { ApiCallSet } from '@/services/api';
@@ -74,6 +76,7 @@ const TumourSummaryEdit = ({
   useEffect(() => {
     if (mutationBurden) {
       setNewMutationBurdenData({
+        role: mutationBurden.role,
         totalMutationsPerMb: mutationBurden.totalMutationsPerMb,
         qualitySvCount: mutationBurden.qualitySvCount,
         qualitySvPercentile: mutationBurden.qualitySvPercentile,
@@ -329,6 +332,22 @@ const TumourSummaryEdit = ({
     if (newMutationBurdenData) {
       return (
         <>
+          <TextField
+            className="tumour-dialog__drop-down"
+            label="Mutation Analysis Role"
+            value={newMutationBurdenData.role}
+            name="role"
+            onChange={handleMutationBurdenChange}
+            variant="outlined"
+            select
+            fullWidth
+          >
+            <MenuItem value={null}>-Select Role-</MenuItem>
+            <MenuItem value={'primary'}>Primary</MenuItem>
+            <MenuItem value={'secondary'}>Secondary</MenuItem>
+            <MenuItem value={'tertiary'}>Tertiary</MenuItem>
+            <MenuItem value={'quarternary'}>Quarternary</MenuItem>
+          </TextField>
           <TextField
             className="tumour-dialog__text-field"
             label="Mutation Burden (Mut/Mb)"
@@ -362,7 +381,56 @@ const TumourSummaryEdit = ({
         </>
       );
     }
-    return null;
+    return (
+      <>
+        <TextField
+          className="tumour-dialog__drop-down"
+          label="Mutation Analysis Role"
+          value={null}
+          name="role"
+          onChange={handleMutationBurdenChange}
+          variant="outlined"
+          select
+          fullWidth
+        >
+          <MenuItem value={null}>-Select Role-</MenuItem>
+          <MenuItem value={'primary'}>Primary</MenuItem>
+          <MenuItem value={'secondary'}>Secondary</MenuItem>
+          <MenuItem value={'tertiary'}>Tertiary</MenuItem>
+          <MenuItem value={'quarternary'}>Quarternary</MenuItem>
+        </TextField>
+        <TextField
+          className="tumour-dialog__text-field"
+          label="Mutation Burden (Mut/Mb)"
+          value={null}
+          name="totalMutationsPerMb"
+          onChange={handleMutationBurdenChange}
+          variant="outlined"
+          fullWidth
+          type="number"
+        />
+        <TextField
+          className="tumour-dialog__text-field"
+          label="SV Burden (POG average)"
+          value={null}
+          name="qualitySvCount"
+          onChange={handleMutationBurdenChange}
+          variant="outlined"
+          fullWidth
+          type="number"
+        />
+        <TextField
+          className="tumour-dialog__text-field"
+          label="SV Burden (Percentile)"
+          value={null}
+          name="qualitySvPercentile"
+          onChange={handleMutationBurdenChange}
+          variant="outlined"
+          fullWidth
+          type="number"
+        />
+      </>
+    );
   }, [newMutationBurdenData, handleMutationBurdenChange]);
 
   const tmburMutBurSection = useMemo(() => {

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 +189,20 @@ const RapidSummary = ({
             PromiseSettledResult<MicrobialType[]>,
           ];
 
+          try {
+            const burdenResp = await api.get(`/reports/${report.ident}/mutation-burden`).request();
+            if (burdenResp[0].qualitySvCount == null) {
+              setPrimaryBurden(null);
+              console.log(burdenResp[0]);
+            } else {
+              setPrimaryBurden(burdenResp[0]);
+              console.log(burdenResp[0]);
+            }
+          } catch (e) {
+            // mutation burden does not exist in records before this implementation, and no backfill will be done on the backend, silent fail this
+            console.error('mutation-burden call error', e?.message);
+          }
+
           if (signaturesResp.status === 'fulfilled') {
             setSignatures(signaturesResp.value);
           } else if (!isPrint) {
@@ -294,6 +309,14 @@ const RapidSummary = ({
     } else {
       msiStatus = null;
     }
+
+    let svBurden: null | string;
+    if (primaryBurden && primaryBurden.qualitySvCount !== null) {
+      svBurden = `${primaryBurden.qualitySvCount} ${primaryBurden.qualitySvPercentile ? `(${primaryBurden.qualitySvPercentile}%)` : ''}`;
+    } else {
+      svBurden = null;
+    }
+
     setTumourSummary([
       {
         term: 'Pathology Tumour Content',
@@ -329,6 +352,10 @@ 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 +367,10 @@ 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 +445,12 @@ 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 +462,10 @@ const RapidSummary = ({
       setReport(newReportData);
     }
 
+    if (newMutationBurdenData) {
+      setPrimaryBurden(newMutationBurdenData);
+    }
+
     if (newTmBurMutBurData) {
       setTmburMutBur(newTmBurMutBurData);
     }
@@ -454,7 +486,7 @@ const RapidSummary = ({
                 <TumourSummaryEdit
                   microbial={microbial}
                   report={report}
-                  mutationBurden={null}
+                  mutationBurden={primaryBurden}
                   tmburMutBur={tmburMutBur}
                   isOpen={showTumourSummaryEdit}
                   onClose={handleTumourSummaryEditClose}