Merge pull request #447 from bcgsc/release/v6.29.0

Release/v6.29.0
bcgsc · Apr 5, 2024 · d9c8598 · d9c8598
2 parents d686662 + a4275a8
commit d9c8598
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Showing 32 changed files with 816 additions and 239 deletions.
diff --git a/app/common.d.ts b/app/common.d.ts
@@ -156,6 +156,7 @@ type CopyNumberType = {
   kbMatches?: KbMatchType<'cnv'>[];
   log2Cna: string | null;
   lohState: string | null;
+  selected: boolean;
   size: number | null;
   start: number | null;
   variantType: 'cnv';
@@ -182,6 +183,7 @@ type StructuralVariantType = {
   ntermGene: string | null;
   ntermTranscript: string | null;
   omicSupport: boolean;
+  selected: boolean;
   svg: string | null;
   svgTitle: string | null;
   variantType: 'sv';
@@ -209,6 +211,7 @@ type SmallMutationType = {
   rnaAltCount: number | null;
   rnaDepth: number | null;
   rnaRefCount: number | null;
+  selected: boolean;
   startPosition: number | null;
   transcript: string | null;
   tumourAltCopies: number | null;
@@ -242,11 +245,14 @@ type ExpOutliersType = {
   primarySitekIQR: number | null;
   rnaReads: number | null;
   rpkm: number | null;
+  selected: boolean;
   tpm: number | null;
   variantType: 'exp';
 } & RecordDefaults;
 
 type TmburType = {
+  adjustedTmb: number | null;
+  adjustedTmbComment: string | null;
   cdsBasesIn1To22AndXAndY: string;
   cdsIndels: number;
   cdsIndelTmb: number;
@@ -255,8 +261,6 @@ type TmburType = {
   comments: string;
   genomeSnvTmb: number;
   genomeIndelTmb: number;
-  adjustedTmb: number | null;
-  adjustedTmbComment: string | null;
   tmbHidden: boolean;
   kbCategory: string | null;
   kbMatches: KbMatchType[];
@@ -314,6 +318,10 @@ type ImmuneType = {
   kbCategory: string | null;
   percentile: number | null;
   score: number | null;
+  pedsPercentile: number | null;
+  pedsScore: number | null;
+  pedsScoreComment: string | null;
+  percentileHidden: boolean;
 } & RecordDefaults;
 
 type MicrobialType = {

diff --git a/app/components/PrintTable/index.scss b/app/components/PrintTable/index.scss
@@ -23,20 +23,22 @@
 
   &__row {
     font-size: 10pt;
-    border-bottom: 1px solid $palette__text--hint;
-    page-break-inside: avoid;
+    border-bottom: 0.5px solid lightgray;
 
     & td {
-      padding: 10px 4px;
+      padding: 3px 4px;
       max-width: 300px;
       overflow-wrap: break-word;
+      break-inside: avoid;
     }
   }
 
   &__none {
     border-bottom: 1px solid $palette__text--hint;
-    padding: 10px 0;
+    padding: 3px 4px;
     text-align: center;
+    border-bottom: 0.5px solid lightgray;
+    font-size: 10pt;
   }
 
   &__cell {

diff --git a/app/components/SignatureCard/index.scss b/app/components/SignatureCard/index.scss
@@ -20,10 +20,12 @@
   }
 
   &-print {
+
     &__group {
       display: inline-flex;
       flex-direction: column;
       margin: 0 auto;
+      max-width: 33%;
     }
 
     &__value {

diff --git a/app/components/SummaryPrintTable/index.tsx b/app/components/SummaryPrintTable/index.tsx
@@ -1,6 +1,7 @@
 import {
   Table, TableCell, TableRow, Typography,
 } from '@mui/material';
+import { Dictionary } from 'lodash';
 import React from 'react';
 
 type SummaryPrintTableProps = {
@@ -11,16 +12,27 @@ type SummaryPrintTableProps = {
   renderValue?: (value: any) => unknown;
 };
 
+const variantTypes = ['cnv', 'smallMutation', 'structuralVariant', 'expression'];
+
+const variantToStrings: Dictionary<string> = {
+  cnv: 'CNV',
+  smallMutation: 'Small Mutation',
+  structuralVariant: 'Structural Variant',
+  expression: 'Expression Outlier',
+};
+
 const SummaryPrintTable = ({
   data,
   labelKey,
   valueKey,
   renderValue = null,
 }: SummaryPrintTableProps) => (
   <Table padding="none" size="small">
-    {data.map(({ [labelKey]: label, [valueKey]: value }) => (
+    {data.filter((key) => (key.value !== null && key.value !== '')).map(({ [labelKey]: label, [valueKey]: value }) => (
       <TableRow>
-        <TableCell><Typography variant="body2" fontWeight="bold">{label}</Typography></TableCell>
+        <TableCell>
+          <Typography variant="body2" fontWeight="bold">{variantTypes.includes(String(label)) ? `${variantToStrings[String(label)]}${Object.values(value).length > 1 ? 's' : ''}` : label}</Typography>
+        </TableCell>
         <TableCell sx={{ paddingLeft: 1 }}>
           {renderValue ? renderValue(value) : value}
         </TableCell>

diff --git a/app/components/TumourSummaryEdit/index.scss b/app/components/TumourSummaryEdit/index.scss
@@ -9,6 +9,11 @@
 
   &__check-box {
     color: gray;
-    padding-top: 2px;
+    margin-top: -12px;
+    font-size: 2;
   }
+}
+
+.checkbox-label {
+  font-size: 10pt;
 }
diff --git a/app/components/TumourSummaryEdit/index.tsx b/app/components/TumourSummaryEdit/index.tsx
@@ -87,6 +87,10 @@ const TumourSummaryEdit = ({
       setNewTCellCd8Data({
         score: tCellCd8.score,
         percentile: tCellCd8.percentile,
+        percentileHidden: tCellCd8.percentileHidden,
+        pedsScore: tCellCd8.pedsScore,
+        pedsPercentile: tCellCd8.pedsPercentile,
+        pedsScoreComment: tCellCd8.pedsScoreComment,
       });
     }
   }, [tCellCd8]);
@@ -95,7 +99,6 @@ const TumourSummaryEdit = ({
     if (mutationBurden) {
       setNewMutationBurdenData({
         role: mutationBurden.role,
-        totalMutationsPerMb: mutationBurden.totalMutationsPerMb,
         qualitySvCount: mutationBurden.qualitySvCount,
         qualitySvPercentile: mutationBurden.qualitySvPercentile,
       });
@@ -126,6 +129,30 @@ const TumourSummaryEdit = ({
     setTCellCd8Dirty(true);
   }, []);
 
+  const handleTCellCd8PercentileVisibleChange = useCallback(({ target: { checked, name } }) => {
+    setNewTCellCd8Data((prevVal) => ({
+      ...prevVal,
+      [name]: checked,
+    }));
+    setTCellCd8Dirty(true);
+  }, []);
+
+  const handlePedsCd8tChange = useCallback(({ target: { value, name } }) => {
+    setNewTCellCd8Data((cd8t) => ({
+      ...cd8t,
+      [name]: parseFloat(value),
+    }));
+    setTCellCd8Dirty(true);
+  }, []);
+
+  const handlePedsCd8tCommentChange = useCallback(({ target: { value, name } }) => {
+    setNewTCellCd8Data((cd8t) => ({
+      ...cd8t,
+      [name]: value,
+    }));
+    setTCellCd8Dirty(true);
+  }, []);
+
   const handleMutationBurdenChange = useCallback((event: React.ChangeEvent<HTMLInputElement>) => {
     const { target: { value, name } } = event;
     setNewMutationBurdenData((prevVal) => ({ ...prevVal, [name]: value }));
@@ -158,11 +185,16 @@ const TumourSummaryEdit = ({
 
   const handleClose = useCallback(async (isSaved) => {
     let callSet = null;
-    if (!!newTmburMutData.adjustedTmb && !newTmburMutData.adjustedTmbComment) {
+    if (!!newTmburMutData?.adjustedTmb && !newTmburMutData?.adjustedTmbComment) {
       snackbar.warning('Please add a comment on the adjusted TMB');
       isSaved = false;
       onClose(false);
     }
+    if (!!newTCellCd8Data?.pedsScore && !newTCellCd8Data?.pedsScoreComment) {
+      snackbar.warning('Please add a comment on the added pediatric CD8+ t cell score');
+      isSaved = false;
+      onClose(false);
+    }
     if (isSaved) {
       setIsApiCalling(true);
       const apiCalls = [];
@@ -359,7 +391,7 @@ const TumourSummaryEdit = ({
         return (
           <TextField
             className="tumour-dialog__text-field"
-            label="Captiv 8 Score"
+            label="CAPTIV-8 Score"
             value={newReportData.captiv8Score}
             name="captiv8Score"
             onChange={handleReportChange}
@@ -430,21 +462,66 @@ const TumourSummaryEdit = ({
         fullWidth
         type="number"
       />
-    </>
-  ), [newTCellCd8Data, handleTCellCd8Change]);
-
-  const mutBurDataSection = useMemo(() => (
-    <>
+      <FormControlLabel
+        className="tumour-dialog__check-box"
+        control={(
+          <Checkbox
+            size="small"
+            icon={<Visibility />}
+            checkedIcon={<VisibilityOff />}
+            checked={newTCellCd8Data?.percentileHidden}
+            name="percentileHidden"
+            onChange={handleTCellCd8PercentileVisibleChange}
+            sx={{
+              color: 'default',
+              '&.Mui-checked': {
+                color: pink[800],
+              },
+              marginLeft: 1,
+            }}
+          />
+        )}
+        label={<div className="checkbox-label">Show/Hide CD8+ Percentile</div>}
+      />
       <TextField
         className="tumour-dialog__text-field"
-        label="Mutation Burden (Mut/Mb)"
-        value={newMutationBurdenData?.totalMutationsPerMb ?? null}
-        name="totalMutationsPerMb"
-        onChange={handleMutationBurdenChange}
+        label="Pediatric CD8+ T Cell Score"
+        value={newTCellCd8Data?.pedsScore ?? null}
+        name="pedsScore"
+        disabled={report.patientInformation.caseType !== 'Pediatric'}
+        onChange={handlePedsCd8tChange}
         variant="outlined"
         fullWidth
         type="number"
       />
+      <TextField
+        className="tumour-dialog__text-field"
+        label="Pediatric CD8+ T Cell Percentile"
+        value={newTCellCd8Data?.pedsPercentile ?? null}
+        name="pedsPercentile"
+        disabled={report.patientInformation.caseType !== 'Pediatric'}
+        onChange={handlePedsCd8tChange}
+        variant="outlined"
+        fullWidth
+        type="number"
+      />
+      <TextField
+        className="tumour-dialog__text-field"
+        label="Pediatric CD8+ T Cell Comment"
+        value={newTCellCd8Data?.pedsScoreComment ?? ''}
+        name="pedsScoreComment"
+        disabled={!newTCellCd8Data?.pedsScore && !newTCellCd8Data?.pedsScoreComment}
+        required={!!newTCellCd8Data?.pedsScore}
+        onChange={handlePedsCd8tCommentChange}
+        variant="outlined"
+        fullWidth
+        type="text"
+      />
+    </>
+  ), [newTCellCd8Data?.score, newTCellCd8Data?.percentile, newTCellCd8Data?.percentileHidden, newTCellCd8Data?.pedsScore, newTCellCd8Data?.pedsPercentile, newTCellCd8Data?.pedsScoreComment, handleTCellCd8Change, handleTCellCd8PercentileVisibleChange, report.patientInformation.caseType, handlePedsCd8tChange, handlePedsCd8tCommentChange]);
+
+  const mutBurDataSection = useMemo(() => (
+    <>
       <TextField
         className="tumour-dialog__text-field"
         label="SV Burden (POG average)"
@@ -516,6 +593,7 @@ const TumourSummaryEdit = ({
         className="tumour-dialog__check-box"
         control={(
           <Checkbox
+            size="small"
             icon={<Visibility />}
             checkedIcon={<VisibilityOff />}
             checked={newTmburMutData?.tmbHidden}
@@ -526,10 +604,11 @@ const TumourSummaryEdit = ({
               '&.Mui-checked': {
                 color: pink[800],
               },
+              marginLeft: 1,
             }}
           />
         )}
-        label="Show/Hide TMB Score"
+        label={<div className="checkbox-label">Show/Hide TMB Information</div>}
       />
     </>
   ), [newTmburMutData?.genomeSnvTmb, newTmburMutData?.genomeIndelTmb, newTmburMutData?.adjustedTmb, newTmburMutData?.adjustedTmbComment, newTmburMutData?.tmbHidden, handleTmburChange, handleAdjustedTmbCommentChange, handleAdjustedTmbVisibleChange]);

diff --git a/app/components/VariantEditDialog/index.scss b/app/components/VariantEditDialog/index.scss
@@ -0,0 +1,6 @@
+.variant-edit-dialog {
+  &__form-control {
+    min-width: 160px;
+    margin: 0 0 16px;
+  }
+}