Merge pull request #416 from bcgsc/bugfix/DEVSU-2148-tumoursummary-fixes

[DEVSU-2148] tumour summary fixes

Author: kttkjl

app/components/TumourSummaryEdit/index.tsx

@@ -137,24 +137,26 @@ const TumourSummaryEdit = ({
 
       if (reportDirty && newReportData) {
         apiCalls.push(api.put(`/reports/${report.ident}`, newReportData, {}));
-      } else {
-        apiCalls.push({ request: () => null });
       }
 
       if (mutationBurdenDirty && newMutationBurdenData) {
         if (mutationBurden?.ident) {
           apiCalls.push(api.put(`/reports/${report.ident}/mutation-burden/${mutationBurden.ident}`, newMutationBurdenData, {}));
         } else {
-          apiCalls.push(api.post(`/reports/${report.ident}/mutation-burden`, newMutationBurdenData, {}));
+          apiCalls.push(api.post(
+            `/reports/${report.ident}/mutation-burden`,
+            { ...newMutationBurdenData, role: 'primary' },
+            {},
+          ));
         }
-      } else {
-        apiCalls.push({ request: () => null });
       }
 
-      if (tmburMutDirty && newTmburMutData && tmburMutBur?.ident) {
-        apiCalls.push(api.put(`/reports/${report.ident}/tmbur-mutation-burden`, newTmburMutData, {}));
-      } else {
-        apiCalls.push({ request: () => null });
+      if (tmburMutDirty && newTmburMutData) {
+        if (tmburMutBur?.ident) {
+          apiCalls.push(api.put(`/reports/${report.ident}/tmbur-mutation-burden`, newTmburMutData, {}));
+        } else {
+          apiCalls.push(api.post(`/reports/${report.ident}/tmbur-mutation-burden`, newTmburMutData, {}));
+        }
       }
 
       callSet = new ApiCallSet(apiCalls);
@@ -164,19 +166,33 @@ 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 tmburMutResp = null;
+          let mutationBurdenResp = null;
+          let reportResp = null;
 
           // Too complicated between delete/update/new, might as well grab updated micb species for report again
-          const microbialResp = await api.get(`/reports/${report.ident}/summary/microbial`).request();
+          if (microbialDirty) {
+            microbialResp = await api.get(`/reports/${report.ident}/summary/microbial`).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();
+          }
+
           snackbar.success('Successfully updated Tumour Summary');
           onClose(
             true,
             microbialDirty ? microbialResp : null,
             reportDirty ? reportResp : null,
-            mutationBurdenDirty ? primaryBurdenResp : null,
+            mutationBurdenDirty ? mutationBurdenResp.find((mb) => mb.role === 'primary') : null,
             tmburMutDirty ? tmburMutResp : null,
           );
         } catch (callSetError) {
@@ -323,53 +339,43 @@ const TumourSummaryEdit = ({
     return null;
   }, [handleClicked, handleDelete, handleKeyDown, newMicrobialData]);
 
-  const mutBurDataSection = useMemo(() => {
-    if (newMutationBurdenData) {
-      return (
-        <TextField
-          className="tumour-dialog__text-field"
-          label="Mutation Burden (Mut/Mb)"
-          value={newMutationBurdenData.totalMutationsPerMb}
-          name="totalMutationsPerMb"
-          onChange={handleMutationBurdenChange}
-          variant="outlined"
-          fullWidth
-          type="number"
-        />
-      );
-    }
-    return null;
-  }, [newMutationBurdenData, handleMutationBurdenChange]);
+  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 tmburMutBurSection = useMemo(() => {
-    if (newTmburMutData) {
-      return (
-        <>
-          <TextField
-            className="tumour-dialog__text-field"
-            label="genomeSnvTmb"
-            value={newTmburMutData.genomeSnvTmb}
-            name="genomeSnvTmb"
-            onChange={handleTmburChange}
-            variant="outlined"
-            fullWidth
-            type="number"
-          />
-          <TextField
-            className="tumour-dialog__text-field"
-            label="genomeIndelTmb"
-            value={newTmburMutData.genomeIndelTmb}
-            name="genomeIndelTmb"
-            onChange={handleTmburChange}
-            variant="outlined"
-            fullWidth
-            type="number"
-          />
-        </>
-      );
-    }
-    return null;
-  }, [newTmburMutData, handleTmburChange]);
+    <>
+      <TextField
+        className="tumour-dialog__text-field"
+        label="genomeSnvTmb"
+        value={newTmburMutData?.genomeSnvTmb ?? 0}
+        name="genomeSnvTmb"
+        onChange={handleTmburChange}
+        variant="outlined"
+        fullWidth
+        type="number"
+      />
+      <TextField
+        className="tumour-dialog__text-field"
+        label="genomeIndelTmb"
+        value={newTmburMutData?.genomeIndelTmb ?? 0}
+        name="genomeIndelTmb"
+        onChange={handleTmburChange}
+        variant="outlined"
+        fullWidth
+        type="number"
+      />
+    </>;
+  }, [newTmburMutData?.genomeSnvTmb, newTmburMutData?.genomeIndelTmb, handleTmburChange]);
 
   return (
     <Dialog open={isOpen}>

app/hooks/useConfirmDialog.tsx

@@ -1,6 +1,5 @@
 import AlertDialog from '@/components/AlertDialog';
 import ReportContext from '@/context/ReportContext';
-import api from '@/services/api';
 import React, { useCallback, useContext } from 'react';
 import ReactDOM from 'react-dom';
 import snackbar from '@/services/SnackbarUtils';

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

@@ -444,12 +444,12 @@ const GenomicSummary = ({
     isSaved: boolean,
     newMicrobialData: MicrobialType[],
     newReportData: ReportType,
-    newMutationBurdenData: MutationBurdenType,
+    newPrimaryBurdenData: MutationBurdenType,
     newTmBurMutBurData: TmburType,
   ) => {
     setShowTumourSummaryEdit(false);
 
-    if (!isSaved || (!newMicrobialData && !newReportData && !newMutationBurdenData && !newTmBurMutBurData)) {
+    if (!isSaved || (!newMicrobialData && !newReportData && !newPrimaryBurdenData && !newTmBurMutBurData)) {
       return;
     }
 
@@ -461,8 +461,8 @@ const GenomicSummary = ({
       setReport(newReportData);
     }
 
-    if (newMutationBurdenData) {
-      setPrimaryBurden(newMutationBurdenData);
+    if (newPrimaryBurdenData) {
+      setPrimaryBurden(newPrimaryBurdenData);
     }
 
     if (newTmBurMutBurData) {