Merge pull request #438 from bcgsc/release/v6.28.0

Release/v6.28.0
bcgsc · Mar 13, 2024 · d686662 · d686662
2 parents b81af1b + 3e02934
commit d686662
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Showing 15 changed files with 187 additions and 50 deletions.
diff --git a/app/common.d.ts b/app/common.d.ts
@@ -255,6 +255,9 @@ type TmburType = {
   comments: string;
   genomeSnvTmb: number;
   genomeIndelTmb: number;
+  adjustedTmb: number | null;
+  adjustedTmbComment: string | null;
+  tmbHidden: boolean;
   kbCategory: string | null;
   kbMatches: KbMatchType[];
   msiScore: number;

diff --git a/app/components/DataTable/index.tsx b/app/components/DataTable/index.tsx
@@ -325,7 +325,7 @@ const DataTable = ({
       colApi.setColumnsVisible(hiddenColumns, false);
     }
 
-    if (rowData.length >= MAX_VISIBLE_ROWS && !isPrint && !isFullLength) {
+    if (rowData.length >= MAX_VISIBLE_ROWS && !isPrint && isFullLength) {
       gridDiv.current.style.height = MAX_TABLE_HEIGHT;
       gridApi?.setDomLayout('normal');
     }
@@ -560,11 +560,11 @@ const DataTable = ({
               paginationAutoPageSize={isFullLength}
               paginationPageSize={MAX_VISIBLE_ROWS}
               autoSizePadding={1}
-              deltaRowDataMode={canReorder}
+              immutableData={canReorder}
               getRowNodeId={(data) => data.ident}
               onRowDragEnd={canReorder ? onRowDragEnd : null}
               editType="fullRow"
-              enableCellTextSelection
+              enableCellTextSelection={!showReorder}
               onFilterChanged={handleFilterAndSortChanged}
               onSortChanged={handleFilterAndSortChanged}
               noRowsOverlayComponent="NoRowsOverlay"

diff --git a/app/components/PrintTable/index.scss b/app/components/PrintTable/index.scss
@@ -3,6 +3,7 @@
 .table {
   border-collapse: collapse;
   margin: 8px;
+  font-family: Arial, Helvetica, sans-serif;
 
   &--full-width {
     width: 100%;

diff --git a/app/components/SignatureCard/SignatureCard.stories.tsx b/app/components/SignatureCard/SignatureCard.stories.tsx
@@ -1,6 +1,6 @@
 import React, { useMemo } from 'react';
 import { action } from '@storybook/addon-actions';
-import { Story } from '@storybook/react/types-6-0';
+import { StoryFn } from '@storybook/react';
 
 import ReportContext from '@/context/ReportContext';
 import SignatureCard, { SignatureCardProps } from '.';
@@ -24,7 +24,7 @@ const Template = (args) => {
   );
 };
 
-export const Unsigned: Story<SignatureCardProps> = Template.bind({});
+export const Unsigned: StoryFn<SignatureCardProps> = Template.bind({});
 
 Unsigned.args = {
   title: 'Author',
@@ -36,7 +36,7 @@ Unsigned.args = {
 
 const signedAt = '2021-12-02T22:05:15.326Z';
 
-export const Signed: Story<SignatureCardProps> = Template.bind({});
+export const Signed: StoryFn<SignatureCardProps> = Template.bind({});
 
 Signed.args = {
   title: 'Author',
@@ -59,6 +59,8 @@ Signed.args = {
     reviewerSignature: null,
     reviewerSignedAt: null,
     updatedAt: signedAt,
+    creatorSignature: null,
+    creatorSignedAt: signedAt,
   },
   type: 'author',
   isPrint: false,

diff --git a/app/components/TumourSummaryEdit/index.scss b/app/components/TumourSummaryEdit/index.scss
@@ -6,4 +6,9 @@
   &__text-field {
     margin: 12px 0;
   }
+
+  &__check-box {
+    color: gray;
+    padding-top: 2px;
+  }
 }
diff --git a/app/components/TumourSummaryEdit/index.tsx b/app/components/TumourSummaryEdit/index.tsx
@@ -10,7 +10,11 @@ import {
   Button,
   Chip,
   Autocomplete,
+  FormControlLabel,
+  Checkbox,
 } from '@mui/material';
+import { Visibility, VisibilityOff } from '@mui/icons-material';
+import { pink } from '@mui/material/colors';
 import cloneDeep from 'lodash/cloneDeep';
 import api, { ApiCallSet } from '@/services/api';
 import ConfirmContext from '@/context/ConfirmContext';
@@ -103,6 +107,9 @@ const TumourSummaryEdit = ({
       setNewTmburMutData({
         genomeSnvTmb: tmburMutBur.genomeSnvTmb,
         genomeIndelTmb: tmburMutBur.genomeIndelTmb,
+        adjustedTmb: tmburMutBur.adjustedTmb,
+        adjustedTmbComment: tmburMutBur.adjustedTmbComment,
+        tmbHidden: tmburMutBur.tmbHidden,
       });
     }
   }, [tmburMutBur]);
@@ -133,8 +140,29 @@ const TumourSummaryEdit = ({
     setTmburMutDirty(true);
   }, []);
 
+  const handleAdjustedTmbCommentChange = useCallback(({ target: { value, name } }) => {
+    setNewTmburMutData((tmb) => ({
+      ...tmb,
+      [name]: value,
+    }));
+    setTmburMutDirty(true);
+  }, []);
+
+  const handleAdjustedTmbVisibleChange = useCallback(({ target: { checked, name } }) => {
+    setNewTmburMutData((tmb) => ({
+      ...tmb,
+      [name]: checked,
+    }));
+    setTmburMutDirty(true);
+  }, []);
+
   const handleClose = useCallback(async (isSaved) => {
     let callSet = null;
+    if (!!newTmburMutData.adjustedTmb && !newTmburMutData.adjustedTmbComment) {
+      snackbar.warning('Please add a comment on the adjusted TMB');
+      isSaved = false;
+      onClose(false);
+    }
     if (isSaved) {
       setIsApiCalling(true);
       const apiCalls = [];
@@ -236,7 +264,6 @@ const TumourSummaryEdit = ({
           );
         } catch (callSetError) {
           snackbar.error(`Error updating Tumour Summary: ${callSetError?.message}`);
-          console.error(callSetError);
         } finally {
           setIsApiCalling(false);
         }
@@ -463,8 +490,49 @@ const TumourSummaryEdit = ({
         fullWidth
         type="number"
       />
+      <TextField
+        className="tumour-dialog__text-field"
+        label="Adjusted TMB"
+        value={newTmburMutData?.adjustedTmb ?? null}
+        name="adjustedTmb"
+        onChange={handleTmburChange}
+        variant="outlined"
+        fullWidth
+        type="number"
+      />
+      <TextField
+        className="tumour-dialog__text-field"
+        label="Adjusted TMB Comment"
+        value={newTmburMutData?.adjustedTmbComment ?? ''}
+        name="adjustedTmbComment"
+        disabled={!newTmburMutData?.adjustedTmb && !newTmburMutData?.adjustedTmbComment}
+        required={!!newTmburMutData?.adjustedTmb}
+        onChange={handleAdjustedTmbCommentChange}
+        variant="outlined"
+        fullWidth
+        type="text"
+      />
+      <FormControlLabel
+        className="tumour-dialog__check-box"
+        control={(
+          <Checkbox
+            icon={<Visibility />}
+            checkedIcon={<VisibilityOff />}
+            checked={newTmburMutData?.tmbHidden}
+            name="tmbHidden"
+            onChange={handleAdjustedTmbVisibleChange}
+            sx={{
+              color: 'default',
+              '&.Mui-checked': {
+                color: pink[800],
+              },
+            }}
+          />
+        )}
+        label="Show/Hide TMB Score"
+      />
     </>
-  ), [newTmburMutData?.genomeSnvTmb, newTmburMutData?.genomeIndelTmb, handleTmburChange]);
+  ), [newTmburMutData?.genomeSnvTmb, newTmburMutData?.genomeIndelTmb, newTmburMutData?.adjustedTmb, newTmburMutData?.adjustedTmbComment, newTmburMutData?.tmbHidden, handleTmburChange, handleAdjustedTmbCommentChange, handleAdjustedTmbVisibleChange]);
 
   return (
     <Dialog open={isOpen}>

diff --git a/app/views/PrintView/index.tsx b/app/views/PrintView/index.tsx
@@ -166,18 +166,29 @@ const Print = ({
       const showPrint = async () => {
         const paged = new Previewer();
         await paged.preview(document.getElementById('root'), ['index.css'], document.body);
+        const templateName = report.template.name === 'probe' ? 'targeted_gene' : report.template.name;
         const currentDate = new Date();
         const year = currentDate.getFullYear();
         const month = (currentDate.getMonth() + 1).toString().padStart(2, '0');
         const day = currentDate.getDate().toString().padStart(2, '0');
         const hours = currentDate.getHours().toString().padStart(2, '0');
         const minutes = currentDate.getMinutes().toString().padStart(2, '0');
         const seconds = currentDate.getSeconds().toString().padStart(2, '0');
-        const { timeZone } = new Intl.DateTimeFormat().resolvedOptions();
+        let serverName;
+        switch (process.env.NODE_ENV) {
+          case 'development':
+            serverName = '_iprdev';
+            break;
+          case 'staging':
+            serverName = '_iprstaging';
+            break;
+          default:
+            serverName = '';
+            break;
+        }
+        const formattedDate = `${year}-${month}-${day}_${hours}h${minutes}m${seconds}s`;
 
-        const formattedDate = `${year}-${month}-${day}-${hours}:${minutes}:${seconds}-${timeZone.replace(/\//g, '_')}`;
-
-        document.title = `${report.patientId}_${report.template.name}_${formattedDate}`;
+        document.title = `${report.patientId}${serverName}_${templateName}_report_${formattedDate}`;
         window.print();
         setIsPrintDialogShown(true);
       };
@@ -228,7 +239,11 @@ const Print = ({
     return null;
   }, [report, theme, template, printVersion]);
 
-  const reportContextValue = useMemo(() => ({ report, setReport }), [report, setReport]);
+  const reportContextValue = useMemo(() => ({
+    canEdit: false,
+    report,
+    setReport,
+  }), [report, setReport]);
 
   return (
     <ReportContext.Provider value={reportContextValue}>

diff --git a/app/views/ReportView/components/AnalystComments/index.scss b/app/views/ReportView/components/AnalystComments/index.scss
@@ -20,6 +20,7 @@
 
   &--print {
     padding: 0;
+    font-family: Arial, Helvetica, sans-serif;
 
     &__user-text {
       padding: 8px 32px;

diff --git a/app/views/ReportView/components/Appendices/index.scss b/app/views/ReportView/components/Appendices/index.scss
@@ -1,6 +1,7 @@
 .appendices {
   margin: 20px auto;
   padding: 0 20px;
+  font-family: Arial, Helvetica, sans-serif;
 
   &__config {
     padding: 16px;

diff --git a/app/views/ReportView/components/GenomicSummary/index.tsx b/app/views/ReportView/components/GenomicSummary/index.tsx
@@ -13,7 +13,6 @@ import sortBy from 'lodash/sortBy';
 
 import api, { ApiCallSet } from '@/services/api';
 import { formatDate } from '@/utils/date';
-import useReport from '@/hooks/useReport';
 import ConfirmContext from '@/context/ConfirmContext';
 import ReadOnlyTextField from '@/components/ReadOnlyTextField';
 import DemoDescription from '@/components/DemoDescription';
@@ -27,8 +26,8 @@ import TumourSummaryEdit from '@/components/TumourSummaryEdit';
 import {
   TumourSummaryType, MicrobialType, ImmuneType, MutationBurdenType, TmburType, MsiType,
 } from '@/common';
-import { SummaryProps } from '@/commonComponents';
 import SummaryPrintTable from '@/components/SummaryPrintTable';
+import useReport from '@/hooks/useReport';
 
 import VariantChips from './components/VariantChips';
 import VariantCounts from './components/VariantCounts';
@@ -72,7 +71,11 @@ const customTypeSort = (variant) => {
   return 3;
 };
 
-type GenomicSummaryProps = Omit<SummaryProps, 'templateName'> & WithLoadingInjectedProps;
+type GenomicSummaryProps = {
+  loadedDispatch?: ({ type }: { type: string }) => void;
+  isPrint: boolean;
+  printVersion?: 'stable' | 'beta' | null;
+} & WithLoadingInjectedProps;
 
 const GenomicSummary = ({
   isPrint = false,
@@ -318,7 +321,7 @@ const GenomicSummary = ({
         },
         {
           term: 'Mutation Burden',
-          value: primaryBurden && primaryBurden.totalMutationsPerMb !== null ? `${primaryBurden.totalMutationsPerMb} mut/Mb` : null,
+          value: primaryBurden && primaryBurden.totalMutationsPerMb !== null && (!tmburMutBur?.adjustedTmb || tmburMutBur.tmbHidden === true) ? `${primaryBurden.totalMutationsPerMb} Mut/Mb` : null,
         },
         {
           term: `SV Burden (${primaryComparator ? primaryComparator.name : 'primary'})`,
@@ -343,10 +346,16 @@ const GenomicSummary = ({
             : null,
         },
         {
-          term: 'Genome TMB (mut/mb)', // float
+          term:
+            tmburMutBur?.adjustedTmb ? 'Adjusted TMB (Mut/Mb)' : 'Genome TMB (Mut/Mb)', // float
           // Forced to do this due to javascript floating point issues
           value:
-            tmburMutBur ? (tmburMutBur.genomeSnvTmb + tmburMutBur.genomeIndelTmb).toFixed(2) : null,
+            tmburMutBur && !tmburMutBur.tmbHidden ? tmburMutBur.adjustedTmb?.toFixed(2) ?? (tmburMutBur.genomeSnvTmb + tmburMutBur.genomeIndelTmb).toFixed(2) : null,
+        },
+        {
+          term: 'Adjusted TMB Comment',
+          value:
+            tmburMutBur?.adjustedTmbComment && !tmburMutBur.tmbHidden ? tmburMutBur.adjustedTmbComment : null,
         },
       ]);
     }
@@ -368,7 +377,6 @@ const GenomicSummary = ({
         snackbar.success('Entry deleted');
       }
     } catch (err) {
-      console.error(err);
       snackbar.error('Entry NOT deleted due to an error');
     }
   }, [report, isSigned, showConfirmDialog]);
@@ -384,7 +392,6 @@ const GenomicSummary = ({
       setVariants((prevVal) => ([...prevVal, categorizedVariantEntry]));
       snackbar.success('Entry added');
     } catch (err) {
-      console.error(err);
       snackbar.error('Entry NOT added due to an error');
     }
   }, [report]);
@@ -610,7 +617,7 @@ const GenomicSummary = ({
         {dataSection}
       </div>
     );
-  }, [canEdit, classNamePrefix, handleTumourSummaryEditClose, microbial, primaryBurden, tmburMutBur, report, showTumourSummaryEdit, tumourSummary, printVersion]);
+  }, [canEdit, classNamePrefix, handleTumourSummaryEditClose, microbial, tCellCd8, primaryBurden, tmburMutBur, report, showTumourSummaryEdit, tumourSummary, printVersion]);
 
   const alterationsSection = useMemo(() => {
     let titleSection = (