Merge pull request #645 from bcgsc/develop

add work to release

Author: elewis2

app/components/TumourSummaryEdit/index.tsx

@@ -24,7 +24,7 @@ import useConfirmDialog from '@/hooks/useConfirmDialog';
 import './index.scss';
 import { ReportType } from '@/context/ReportContext';
 import {
-  ImmuneType, MicrobialType, MutationBurdenType, TmburType,
+  ImmuneType, MicrobialType, MsiType, MutationBurdenType, TmburType,
 } from '@/common';
 import snackbar from '@/services/SnackbarUtils';
 import { getMicbSiteIntegrationStatusLabel } from '@/utils/getMicbSiteIntegrationStatusLabel';
@@ -41,6 +41,7 @@ type TumourSummaryEditProps = {
   tCellCd8: ImmuneType;
   mutationBurden: MutationBurdenType;
   tmburMutBur: TmburType;
+  msi?: MsiType;
   isOpen: boolean;
   onEditClose: (
     isSaved: boolean,
@@ -49,6 +50,7 @@ type TumourSummaryEditProps = {
     newTCellCd8Data?: ImmuneType,
     newMutationBurdenData?: MutationBurdenType,
     newTmBurMutBurData?: TmburType,
+    newMsiData?: MsiType,
   ) => void;
 };
 
@@ -61,6 +63,7 @@ const TumourSummaryEdit = ({
   tCellCd8,
   mutationBurden,
   tmburMutBur,
+  msi,
   isOpen,
   onEditClose,
 }: TumourSummaryEditProps): JSX.Element => {
@@ -72,11 +75,13 @@ const TumourSummaryEdit = ({
   const [newTCellCd8Data, setNewTCellCd8Data] = useState<Partial<ImmuneType>>(null);
   const [newMutationBurdenData, setNewMutationBurdenData] = useState<Partial<MutationBurdenType>>(null);
   const [newTmburMutData, setNewTmburMutData] = useState<Partial<TmburType>>(null);
+  const [newMsiData, setNewMsiData] = useState<Partial<MsiType>>(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 [msiDirty, setMsiDirty] = useState(false);
   const [isApiCalling, setIsApiCalling] = useState(false);
 
   useEffect(() => {
@@ -129,10 +134,19 @@ const TumourSummaryEdit = ({
         adjustedTmb: tmburMutBur.adjustedTmb,
         adjustedTmbComment: tmburMutBur.adjustedTmbComment,
         tmbHidden: tmburMutBur.tmbHidden,
+        msiScore: tmburMutBur.msiScore,
       });
     }
   }, [tmburMutBur]);
 
+  useEffect(() => {
+    if (msi) {
+      setNewMsiData({
+        score: msi.score,
+      });
+    }
+  }, [msi]);
+
   const handleReportChange = useCallback((event: React.ChangeEvent<HTMLInputElement>) => {
     const { target: { value, name } } = event;
     setNewReportData((prevVal) => ({ ...prevVal, [name]: value }));
@@ -189,6 +203,16 @@ const TumourSummaryEdit = ({
     setTmburMutDirty(true);
   }, []);
 
+  const handleMsiScoreChange = useCallback((event: React.ChangeEvent<HTMLInputElement>) => {
+    const { target: { value, name } } = event;
+    setNewMsiData((prevVal) => ({ ...prevVal, [name]: value }));
+    if (msi) {
+      setMsiDirty(true);
+    } else if (tmburMutBur) {
+      setTmburMutDirty(true);
+    }
+  }, []);
+
   const handleAdjustedTmbCommentChange = useCallback(({ target: { value, name } }) => {
     setNewTmburMutData((tmb) => ({
       ...tmb,
@@ -291,6 +315,14 @@ const TumourSummaryEdit = ({
         }
       }
 
+      if (msiDirty && newMsiData) {
+        if (msi?.ident) {
+          apiCalls.push(api.put(`/reports/${report.ident}/msi/${msi.ident}`, newMsiData, {}));
+        } else {
+          apiCalls.push(api.post(`/reports/${report.ident}/msi`, newMsiData, {}));
+        }
+      }
+
       callSet = new ApiCallSet(apiCalls);
 
       if (isSigned) {
@@ -303,6 +335,7 @@ const TumourSummaryEdit = ({
           let microbialResp = null;
           let immuneResp = null;
           let tmburMutResp = null;
+          let msiResp = null;
           let mutationBurdenResp = null;
           let reportResp = null;
 
@@ -315,6 +348,9 @@ const TumourSummaryEdit = ({
           if (tmburMutDirty) {
             tmburMutResp = await api.get(`/reports/${report.ident}/tmbur-mutation-burden`).request();
           }
+          if (msiDirty) {
+            msiResp = await api.get(`/reports/${report.ident}/msi`).request();
+          }
           if (mutationBurdenDirty) {
             mutationBurdenResp = await api.get(`/reports/${report.ident}/mutation-burden`).request();
           }
@@ -330,6 +366,7 @@ const TumourSummaryEdit = ({
             tCellCd8Dirty ? immuneResp.find(({ cellType }) => cellType === 'T cells CD8') : null,
             mutationBurdenDirty ? mutationBurdenResp.find((mb) => mb.role === 'primary') : null,
             tmburMutDirty ? tmburMutResp : null,
+            msiDirty ? msiResp : null,
           );
         } catch (callSetError) {
           snackbar.error(`Error updating Tumour Summary: ${callSetError?.message}`);
@@ -351,13 +388,16 @@ const TumourSummaryEdit = ({
     newMutationBurdenData,
     tmburMutDirty,
     newTmburMutData,
+    msiDirty,
+    newMsiData,
     isSigned,
     newMicrobialData,
     microbial,
     report?.ident,
     tCellCd8?.ident,
     mutationBurden?.ident,
     tmburMutBur?.ident,
+    msi?.ident,
     showConfirmDialog,
     onEditClose,
   ]);
@@ -732,6 +772,39 @@ const TumourSummaryEdit = ({
     handleAdjustedTmbVisibleChange,
   ]);
 
+  const msiSection = useMemo(() => (
+    <>
+      {msi && 
+        <TextField
+          className="tumour-dialog__number-field"
+          label="MSI Score"
+          value={newMsiData?.score ?? null}
+          name="score"
+          onChange={handleMsiScoreChange}
+          variant="outlined"
+          fullWidth
+          type="number"
+        /> 
+      }
+      {!msi && tmburMutBur &&
+        <TextField
+          className="tumour-dialog__number-field"
+          label="MSI Score"
+          value={newTmburMutData?.msiScore ?? null}
+          name="msiScore"
+          onChange={handleMsiScoreChange}
+          variant="outlined"
+          fullWidth
+          type="number"
+        />
+      }
+    </>
+  ), [
+    newMsiData?.score,
+    newTmburMutData?.msiScore,
+    handleMsiScoreChange,
+  ]);
+
   return (
     <Dialog open={isOpen}>
       <DialogTitle>
@@ -743,6 +816,7 @@ const TumourSummaryEdit = ({
         {tCellCd8DataSection}
         {mutBurDataSection}
         {tmburMutBurSection}
+        {msiSection}
       </DialogContent>
       <DialogActions>
         <Button onClick={() => handleClose(false)}>

app/utils/getMostCurrentObj.js

@@ -0,0 +1,11 @@
+function getMostCurrentObj(array) {
+  let mostRecentObject = array[0];
+  for (let i = 1; i < array.length; i++) {
+    if (new Date(array[i].createdAt) > new Date(mostRecentObject.createdAt)) {
+      mostRecentObject = array[i];
+    }
+  }
+  return mostRecentObject;
+}
+
+export default getMostCurrentObj;

app/views/AdminView/components/Users/index.tsx

@@ -10,7 +10,6 @@ import snackbar from '@/services/SnackbarUtils';
 import { ErrorMixin } from '@/services/errors/errors';
 import columnDefs from './columnDefs';
 import AddEditUserDialog from './components/AddEditUserDialog';
-
 import './index.scss';
 
 const fetchUsers = async () => {
@@ -46,7 +45,7 @@ const Users = (): JSX.Element => {
   const handleDelete = useCallback((rowData) => {
     if (rowData.ident) {
       // TODO: Add an actual dialog whenever time allows
-      // eslint-disable-next-line no-restricted-globals
+      // eslint-disable-next-line no-restricted-globals, no-alert
       if (confirm(`Are you sure you want to remove this user (${rowData.username})?`)) {
         deleteUserMutation.mutate(rowData.ident);
       } else {