Merge branch 'develop' into feat/DEVSU-2094-rid-displayName-rapid

bcgsc · Oct 20, 2023 · d5a8f75 · d5a8f75
2 parents a533add + 6a4b866
commit d5a8f75
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Showing 5 changed files with 33 additions and 9 deletions.
diff --git a/app/views/GermlineView/components/Report/columnDefs.ts b/app/views/GermlineView/components/Report/columnDefs.ts
@@ -56,15 +56,18 @@ const columnDefs = [
     hide: false,
   },
   {
+    headerName: 'dbSnpIds',
     field: 'dbSnpIds',
     hide: false,
   },
   {
+    headerName: 'clinvarIds',
     field: 'clinvarIds',
     minWidth: 80,
     hide: false,
   },
   {
+    headerName: 'cosmicIds',
     field: 'cosmicIds',
     hide: false,
   },

diff --git a/app/views/GermlineView/components/Report/index.tsx b/app/views/GermlineView/components/Report/index.tsx
@@ -9,10 +9,8 @@ import {
   IconButton,
   Menu,
   MenuItem,
-  Button,
 } from '@mui/material';
 import { AgGridReact } from '@ag-grid-community/react';
-import { ICellRendererParams } from '@ag-grid-community/core';
 import MoreHorizIcon from '@mui/icons-material/MoreHoriz';
 import useGrid from '@/hooks/useGrid';
 import api from '@/services/api';
@@ -134,7 +132,7 @@ const GermlineReport = ({
         .filter((col) => col.getColDef().headerName !== 'Actions' && col.getColDef().headerName)
         .map((col) => col.getColId()),
       fileName: `ipr_${report.patientId}_${report.ident}_germline_${date}.tsv`,
-      processCellCallback: (({ value }) => (typeof value === 'string' ? value?.replace(/,/g, '') : value)),
+      processCellCallback: (({ value }) => (typeof value === 'string' ? value?.replace(/[,\n]/g, ' ') : value)),
     });
   }, [colApi, gridApi, report]);
 

diff --git a/app/views/PrintView/index.tsx b/app/views/PrintView/index.tsx
@@ -150,6 +150,15 @@ const Print = (): JSX.Element => {
       const printTitle = REPORT_TYPE_TO_TITLE[template.name];
       const headerSubtitle = report.patientId;
       const headerSubtitleSuffix = REPORT_TYPE_TO_SUFFIX[template.name];
+
+      let biopsyText = startCase(report?.biopsyName || 'No Biopsy Name');
+      if (report?.patientInformation?.diagnosis) {
+        biopsyText = biopsyText.concat(`- ${startCase(report.patientInformation.diagnosis)}`);
+      }
+      if (report?.patientInformation?.tumourSample && report?.patientInformation?.tumourSample.toLowerCase() !== 'undetermined') {
+        biopsyText = biopsyText.concat(`(${report.patientInformation.tumourSample})`);
+      }
+
       return (
         <div className="print__headers">
           <div className="print__header-left">
@@ -163,11 +172,7 @@ const Print = (): JSX.Element => {
               {`${headerSubtitle}${headerSubtitleSuffix ? ` - ${headerSubtitleSuffix}` : ''}`}
             </Typography>
             <Typography variant="h5">
-              {`${startCase(report.biopsyName || 'No Biopsy Name')} ${
-                report.patientInformation.diagnosis ? `- ${startCase(report.patientInformation.diagnosis)}` : ''
-              } ${
-                report.patientInformation.tumourSample ? `(${report.patientInformation.tumourSample})` : ''
-              }`}
+              {biopsyText}
             </Typography>
           </div>
         </div>

diff --git a/app/views/ReportView/components/RapidSummary/index.tsx b/app/views/ReportView/components/RapidSummary/index.tsx
@@ -594,7 +594,15 @@ const RapidSummary = ({
       return (
         <Box display="flex" flexDirection="row" flexWrap="wrap" margin="1rem 0 1rem 0">
           {
-            (unknownSignificanceResults).map((entry) => (
+            (unknownSignificanceResults).sort(({ displayName: displayNameA }, { displayName: displayNameB }) => {
+              if (displayNameA < displayNameB) {
+                return -1;
+              }
+              if (displayNameA > displayNameB) {
+                return 1;
+              }
+              return 0;
+            }).map((entry) => (
               <Box
                 display="inline-block"
                 padding={1}

diff --git a/app/views/ReportView/components/SmallMutations/columnDefs.ts b/app/views/ReportView/components/SmallMutations/columnDefs.ts
@@ -79,6 +79,11 @@ const columnDefs: ColDef[] = [{
   colId: 'primarySiteFoldChange',
   valueGetter: 'data.gene.expressionVariants.primarySiteFoldChange',
   hide: true,
+}, {
+  headerName: 'Primary Site Z-Score',
+  colId: 'primarySiteZScore',
+  valueGetter: 'data.gene.expressionVariants.primarySiteZScore',
+  hide: true,
 }, {
   headerName: 'Expression (TPM)',
   colId: 'tpm',
@@ -93,6 +98,11 @@ const columnDefs: ColDef[] = [{
   colId: 'diseasekIQR',
   valueGetter: 'data.gene.expressionVariants.diseasekIQR',
   hide: true,
+}, {
+  headerName: 'Disease Z-score',
+  colId: 'diseaseZScore',
+  valueGetter: 'data.gene.expressionVariants.diseaseZScore',
+  hide: true,
 }, {
   headerName: 'Actions',
   colId: 'actions',