DEVSU-2213 Jacky Review

bnguyen-bcgsc · bnguyen-bcgsc · commit 55d80db2bd3c · 2024-02-09T15:01:46.000-08:00
The bugs occurring include:
- tCellCd8 default values in the text fields not available
- tCellCd8 ident not found even though it exists, making the handle does POST instead of PUT
diff --git a/app/components/TumourSummaryEdit/index.tsx b/app/components/TumourSummaryEdit/index.tsx
@@ -19,19 +19,21 @@ import useConfirmDialog from '@/hooks/useConfirmDialog';
 
 import './index.scss';
 import { ReportType } from '@/context/ReportContext';
-import { MicrobialType, MutationBurdenType, TmburType } from '@/common';
+import { ImmuneType, MicrobialType, MutationBurdenType, TmburType } from '@/common';
 import snackbar from '@/services/SnackbarUtils';
 
 type TumourSummaryEditProps = {
   microbial: MicrobialType[];
   report: ReportType;
+  tCellCd8: ImmuneType;
   mutationBurden: MutationBurdenType;
-  tmburMutBur?: TmburType;
+  tmburMutBur: TmburType;
   isOpen: boolean;
   onClose: (
     isSaved: boolean,
     newMicrobialData?: MicrobialType[],
     newReportData?: ReportType,
+    newTCellCd8Data?: ImmuneType,
     newMutationBurdenData?: MutationBurdenType,
     newTmBurMutBurData?: TmburType,
   ) => void;
@@ -43,6 +45,7 @@ const TumourSummaryEdit = ({
   report: {
     template: { name: reportType },
   },
+  tCellCd8,
   mutationBurden,
   tmburMutBur,
   isOpen,
@@ -53,10 +56,12 @@ const TumourSummaryEdit = ({
 
   const [newMicrobialData, setNewMicrobialData] = useState(cloneDeep(microbial));
   const [newReportData, setNewReportData] = useState<Partial<ReportType>>(null);
+  const [newTCellCd8Data, setNewTCellCd8Data] = useState<Partial<ImmuneType>>(null);
   const [newMutationBurdenData, setNewMutationBurdenData] = useState<Partial<MutationBurdenType>>(null);
   const [newTmburMutData, setNewTmburMutData] = useState<Partial<TmburType>>(null);
   const [microbialDirty, setMicrobialDirty] = useState(false);
   const [reportDirty, setReportDirty] = useState(false);
+  const [tCellCd8Dirty, setTCellCd8Dirty] = useState(false);
   const [mutationBurdenDirty, setMutationBurdenDirty] = useState(false);
   const [tmburMutDirty, setTmburMutDirty] = useState(false);
   const [isApiCalling, setIsApiCalling] = useState(false);
@@ -71,6 +76,15 @@ const TumourSummaryEdit = ({
     }
   }, [report]);
 
+  useEffect(() => {
+    if (tCellCd8) {
+      setNewTCellCd8Data({
+        score: tCellCd8.score,
+        percentile: tCellCd8.percentile,
+      });
+    }
+  }, [tCellCd8]);
+
   useEffect(() => {
     if (mutationBurden) {
       setNewMutationBurdenData({
@@ -97,6 +111,12 @@ const TumourSummaryEdit = ({
     setReportDirty(true);
   }, []);
 
+  const handleTCellCd8Change = useCallback((event: React.ChangeEvent<HTMLInputElement>) => {
+    const { target: { value, name } } = event;
+    setNewTCellCd8Data((prevVal) => ({ ...prevVal, [name]: value }));
+    setTCellCd8Dirty(true);
+  }, []);
+
   const handleMutationBurdenChange = useCallback((event: React.ChangeEvent<HTMLInputElement>) => {
     const { target: { value, name } } = event;
     setNewMutationBurdenData((prevVal) => ({ ...prevVal, [name]: value }));
@@ -144,6 +164,16 @@ const TumourSummaryEdit = ({
         apiCalls.push({ request: () => null });
       }
 
+      if (tCellCd8Dirty && newTCellCd8Data) {
+        if (tCellCd8?.ident) {
+          apiCalls.push(api.put(`/reports/${report.ident}/immune-cell-types/${tCellCd8.ident}`, newTCellCd8Data, {}));
+        } else {
+          apiCalls.push(api.post(`/reports/${report.ident}/immune-cell-types`, { ...newTCellCd8Data, cellType: 'T cells CD8' }, {}));
+        }
+      } else {
+        apiCalls.push({ request: () => null });
+      }
+
       if (mutationBurdenDirty && newMutationBurdenData) {
         if (mutationBurden?.ident) {
           apiCalls.push(api.put(`/reports/${report.ident}/mutation-burden/${mutationBurden.ident}`, newMutationBurdenData, {}));
@@ -168,19 +198,37 @@ const TumourSummaryEdit = ({
         setIsApiCalling(false);
       } else {
         try {
-          const resp = await callSet.request();
-          const tmburMutResp = resp.pop();
-          const primaryBurdenResp = resp.pop();
-          const reportResp = resp.pop();
+          await callSet.request();
+
+          let microbialResp = null;
+          let immuneResp = null;
+          let tmburMutResp = null;
+          let mutationBurdenResp = null;
+          let reportResp = null;
+
+          if (microbialDirty) {
+            microbialResp = await api.get(`/reports/${report.ident}/summary/microbial`).request();
+          }
+          if (tCellCd8Dirty) {
+            immuneResp = await api.get(`/reports/${report.ident}/immune-cell-types`).request();
+          }
+          if (tmburMutDirty) {
+            tmburMutResp = await api.get(`/reports/${report.ident}/tmbur-mutation-burden`).request();
+          }
+          if (mutationBurdenDirty) {
+            mutationBurdenResp = await api.get(`/reports/${report.ident}/mutation-burden`).request();
+          }
+          if (reportDirty) {
+            reportResp = await api.get(`/reports/${report.ident}`).request();
+          }
 
-          // Too complicated between delete/update/new, might as well grab updated micb species for report again
-          const microbialResp = await api.get(`/reports/${report.ident}/summary/microbial`).request();
           snackbar.success('Successfully updated Tumour Summary');
           onClose(
             true,
             microbialDirty ? microbialResp : null,
+            tCellCd8Dirty ? immuneResp.find(({cellType})  => cellType === 'T cells CD8') : null,
             reportDirty ? reportResp : null,
-            mutationBurdenDirty ? primaryBurdenResp : null,
+            mutationBurdenDirty ? mutationBurdenResp.find((mb) => mb.role === 'primary') : null,
             tmburMutDirty ? tmburMutResp : null,
           );
         } catch (callSetError) {
@@ -198,6 +246,8 @@ const TumourSummaryEdit = ({
     microbialDirty,
     reportDirty,
     newReportData,
+    tCellCd8Dirty,
+    newTCellCd8Data,
     mutationBurdenDirty,
     newMutationBurdenData,
     tmburMutDirty,
@@ -206,6 +256,7 @@ const TumourSummaryEdit = ({
     newMicrobialData,
     microbial,
     report?.ident,
+    tCellCd8?.ident,
     mutationBurden?.ident,
     tmburMutBur?.ident,
     showConfirmDialog,
@@ -327,13 +378,40 @@ const TumourSummaryEdit = ({
     return null;
   }, [handleClicked, handleDelete, handleKeyDown, newMicrobialData]);
 
+  const tCellCd8DataSection = useMemo(() => {
+    return (
+      <>
+        <TextField
+          className="tumour-dialog__text-field"
+          label="CD8+ T Cell Score"
+          value={newTCellCd8Data?.score ?? 0}
+          name="score"
+          onChange={handleTCellCd8Change}
+          variant="outlined"
+          fullWidth
+          type="number"
+        />
+        <TextField
+          className="tumour-dialog__text-field"
+          label="CD8+ T Cell Percentile"
+          value={newTCellCd8Data?.percentile ?? 0}
+          name="percentile"
+          onChange={handleTCellCd8Change}
+          variant="outlined"
+          fullWidth
+          type="number"
+        />
+      </>
+    )
+  }, [newTCellCd8Data, handleTCellCd8Change])
+
   const mutBurDataSection = useMemo(() => {
     return (
       <>
         <TextField
           className="tumour-dialog__text-field"
           label="Mutation Burden (Mut/Mb)"
-          value={newMutationBurdenData?.totalMutationsPerMb ?? null}
+          value={newMutationBurdenData?.totalMutationsPerMb ?? 0}
           name="totalMutationsPerMb"
           onChange={handleMutationBurdenChange}
           variant="outlined"
@@ -343,7 +421,7 @@ const TumourSummaryEdit = ({
         <TextField
           className="tumour-dialog__text-field"
           label="SV Burden (POG average)"
-          value={newMutationBurdenData?.qualitySvCount ?? null}
+          value={newMutationBurdenData?.qualitySvCount ?? 0}
           name="qualitySvCount"
           onChange={handleMutationBurdenChange}
           variant="outlined"
@@ -353,7 +431,7 @@ const TumourSummaryEdit = ({
         <TextField
           className="tumour-dialog__text-field"
           label="SV Burden (Percentile)"
-          value={newMutationBurdenData?.qualitySvPercentile ?? null}
+          value={newMutationBurdenData?.qualitySvPercentile ?? 0}
           name="qualitySvPercentile"
           onChange={handleMutationBurdenChange}
           variant="outlined"
@@ -370,7 +448,7 @@ const TumourSummaryEdit = ({
         <TextField
           className="tumour-dialog__text-field"
           label="genomeSnvTmb"
-          value={newTmburMutData?.genomeSnvTmb ?? null}
+          value={newTmburMutData?.genomeSnvTmb ?? 0}
           name="genomeSnvTmb"
           onChange={handleTmburChange}
           variant="outlined"
@@ -380,7 +458,7 @@ const TumourSummaryEdit = ({
         <TextField
           className="tumour-dialog__text-field"
           label="genomeIndelTmb"
-          value={newTmburMutData?.genomeIndelTmb ?? null}
+          value={newTmburMutData?.genomeIndelTmb ?? 0}
           name="genomeIndelTmb"
           onChange={handleTmburChange}
           variant="outlined"
@@ -399,6 +477,7 @@ const TumourSummaryEdit = ({
       <DialogContent className="tumour-dialog__content">
         {reportDataSection}
         {micbDataSection}
+        {tCellCd8DataSection}
         {mutBurDataSection}
         {tmburMutBurSection}
       </DialogContent>
diff --git a/app/views/ReportView/components/GenomicSummary/index.tsx b/app/views/ReportView/components/GenomicSummary/index.tsx
@@ -164,7 +164,7 @@ const GenomicSummary = ({
 
           setPrimaryComparator(comparatorsResp.find(({ analysisRole }) => analysisRole === 'mutation burden (primary)'));
           setPrimaryBurden(burdenResp.find((entry: Record<string, unknown>) => entry.role === 'primary'));
-          setTCellCd8(immuneResp.find(({ cellType }) => cellType === 'T cells CD8'));
+          setTCellCd8(immuneResp.find(({cellType})  => cellType === 'T cells CD8'));
           setSignatures(signaturesResp);
 
           if (microbialResp.length) {
@@ -445,12 +445,13 @@ const GenomicSummary = ({
     isSaved: boolean,
     newMicrobialData: MicrobialType[],
     newReportData: ReportType,
+    newTCellCd8Data: ImmuneType,
     newMutationBurdenData: MutationBurdenType,
     newTmBurMutBurData: TmburType,
   ) => {
     setShowTumourSummaryEdit(false);
 
-    if (!isSaved || (!newMicrobialData && !newReportData && !newMutationBurdenData && !newTmBurMutBurData)) {
+    if (!isSaved || (!newMicrobialData && !newReportData && !newTCellCd8Data && !newMutationBurdenData && !newTmBurMutBurData)) {
       return;
     }
 
@@ -462,6 +463,10 @@ const GenomicSummary = ({
       setReport(newReportData);
     }
 
+    if (newTCellCd8Data) {
+      setTCellCd8(newTCellCd8Data)
+    }
+
     if (newMutationBurdenData) {
       setPrimaryBurden(newMutationBurdenData);
     }
