Merge pull request #333 from bcgsc/release/v6.20.0

Release/v6.20.0

Author: kttkjl

app/common.d.ts

@@ -116,30 +116,30 @@ type GeneType = {
 };
 
 type KbMatchType<T extends AnyVariantType = AnyVariantType> = {
-  category: string;
   approvedTherapy: boolean;
-  kbVariant: string;
-  disease: string;
-  relevance: string;
+  category: string;
   context: string;
-  status: string;
-  reference: string;
-  sample: string;
-  inferred: boolean;
+  disease: string;
   evidenceLevel: string;
+  externalSource: string;
+  externalStatementId: string;
+  inferred: boolean;
   iprEvidenceLevel: string;
-  matchedCancer: boolean;
-  pmidRef: string;
-  variantType: T;
-  variant: VariantTypeMap<T>;
-  kbVariantId: string;
-  kbStatementId: string;
   kbData: {
     inferred: boolean;
-  }
-  externalSource: string;
-  externalStatementId: string;
+  } | null;
+  kbStatementId: string;
+  kbVariant: string;
+  kbVariantId: string;
+  matchedCancer: boolean;
+  pmidRef: string;
+  reference: string;
+  relevance: string;
   reviewStatus: string;
+  sample: string | null;
+  status: string | null;
+  variant?: VariantTypeMap<T>;
+  variantType: T;
 } & RecordDefaults;
 
 type CopyNumberType = {
@@ -151,10 +151,12 @@ type CopyNumberType = {
   end: number | null;
   gene: GeneType | null;
   kbCategory: string | null;
+  kbMatches?: VariantTypeMap<'cnv'>[];
   log2Cna: string | null;
   lohState: string | null;
   size: number | null;
   start: number | null;
+  variantType: 'cnv';
 } & RecordDefaults;
 
 type StructuralVariantType = {
@@ -171,13 +173,15 @@ type StructuralVariantType = {
   gene1: GeneType | null;
   gene2: GeneType | null;
   highQuality: boolean;
+  kbMatches?: KbMatchType<'sv'>[];
   mavis_product_id: number | null;
   name: string | null;
   ntermGene: string | null;
   ntermTranscript: string | null;
   omicSupport: boolean;
   svg: string | null;
   svgTitle: string | null;
+  variantType: 'sv';
 } & RecordDefaults;
 
 type SmallMutationType = {
@@ -190,6 +194,7 @@ type SmallMutationType = {
   hgvsCds: string | null;
   hgvsGenomic: string | null;
   hgvsProtein: string | null;
+  kbMatches?: KbMatchType<'mut'>[];
   library: string | null;
   ncbiBuild: string | null;
   normalAltCount: number | null;
@@ -208,6 +213,7 @@ type SmallMutationType = {
   tumourRefCopies: number | null;
   tumourRefCount: number | null;
   zygosity: string | null;
+  variantType: 'mut';
 } & RecordDefaults;
 
 type ExpOutliersType = {
@@ -233,6 +239,7 @@ type ExpOutliersType = {
   rnaReads: number | null;
   rpkm: number | null;
   tpm: number | null;
+  variantType: 'exp';
 } & RecordDefaults;
 
 type TmburType = {
@@ -279,6 +286,34 @@ type TumourSummaryType = {
   action?: () => void | null;
 };
 
+type MutationBurdenType = {
+  codingIndelPercentile: number | null;
+  codingIndelsCount: number | null;
+  codingSnvCount: number | null;
+  codingSnvPercentile: number | null;
+  frameshiftIndelsCount: number | null;
+  qualitySvCount: number | null;
+  qualitySvExpressedCount: number | null;
+  qualitySvPercentile: number | null;
+  role: string;
+  totalIndelCount: number | null;
+  totalMutationsPerMb: number | null;
+  totalSnvCount: number | null;
+  truncatingSnvCount: number | null;
+} & RecordDefaults;
+
+type ImmuneType = {
+  cellType: string | null;
+  kbCategory: string | null;
+  percentile: number | null;
+  score: number | null;
+} & RecordDefaults;
+
+type MicrobialType = {
+  integrationSite: string | null;
+  species: string | null;
+} & RecordDefaults;
+
 type AppendixType = RecordDefaults & {
   text: string;
 };
@@ -302,4 +337,7 @@ export {
   TumourSummaryType,
   TmburType,
   MsiType,
+  MutationBurdenType,
+  ImmuneType,
+  MicrobialType,
 };

app/components/DataTable/components/ArrayCellRenderer/__tests__/ArrayCellRenderer.test.ts

@@ -58,7 +58,7 @@ describe('ArrayCellRenderer', () => {
 
     const elem = await screen.findByText(mockLinkArrayData.test[0]);
 
-    expect(elem).toHaveAttribute('href', `http://${mockLinkArrayData.test[0]}`);
-    expect(screen.queryByText(`http://${mockLinkArrayData.test[1]}`)).toBeNull();
+    expect(elem).toHaveAttribute('href', `${mockLinkArrayData.test[0]}`);
+    expect(screen.queryByText(`${mockLinkArrayData.test[1]}`)).toBeNull();
   });
 });

app/components/DataTable/components/ArrayCellRenderer/index.tsx

@@ -4,25 +4,45 @@ import { ICellRendererParams } from '@ag-grid-community/core';
 
 import './index.scss';
 
+const urlRegex = /^(?:https?:\/\/)?(?:[\w-]+\.)+[a-z]{2,}(?:\/[\w\-\.\/]*)*$/i;
+
 const RenderArrayCell = (field: string, isLink: boolean): (cellParams: ICellRendererParams) => JSX.Element => {
   if (isLink) {
-    return function ArrayCell(cellParams) {
-      if (Array.isArray(cellParams.data[field])) {
-        const cellData = [...cellParams.data[field]].sort();
-        const firstVal = cellData[0].replace(/(pmid:)|(#)/, '');
+    return function ArrayCell({ data }: ICellRendererParams) {
+      if (Array.isArray(data[field])) {
+        const cellData = [...data[field]].sort();
 
-        return (
-          <div>
+        const firstVal = cellData[0]?.replace(/(pmid:)|(#)/, '');
+
+        let link = firstVal;
+        let validLink = false;
+
+        // firstVal might be non-link
+        if (firstVal.match(/^\d+$/)) {
+          link = `https://ncbi.nlm.nih.gov/pubmed/${firstVal}`;
+          validLink = true;
+        } else if (urlRegex.test(firstVal)) {
+          validLink = true;
+        }
+
+        let linkComponent = firstVal;
+
+        if (validLink) {
+          linkComponent = (
             <a
               className="array-cell__link"
-              href={(firstVal.match(/^\d+$/))
-                ? `https://ncbi.nlm.nih.gov/pubmed/${firstVal}`
-                : `http://${firstVal}`}
+              href={link}
               rel="noopener noreferrer"
               target="_blank"
             >
               {firstVal}
             </a>
+          );
+        }
+
+        return (
+          <div>
+            {linkComponent}
             {cellData.length > 1 && (
               <>
                 …
@@ -33,15 +53,15 @@ const RenderArrayCell = (field: string, isLink: boolean): (cellParams: ICellRend
       }
       return (
         <div>
-          {cellParams.data[field]}
+          {data[field]}
         </div>
       );
     };
   }
 
-  return function ArrayCell(cellParams) {
-    if (Array.isArray(cellParams.data[field])) {
-      const cellData = [...cellParams.data[field]].sort();
+  return function ArrayCell({ data }: ICellRendererParams) {
+    if (Array.isArray(data[field])) {
+      const cellData = [...data[field]].sort();
       const [firstVal] = cellData;
 
       if (typeof firstVal === 'string') {
@@ -61,7 +81,7 @@ const RenderArrayCell = (field: string, isLink: boolean): (cellParams: ICellRend
     }
     return (
       <div>
-        {`${cellParams.data[field] === null ? '' : cellParams.data[field]}`}
+        {`${data[field] === null ? '' : data[field]}`}
       </div>
     );
   };

app/components/DataTable/components/CivicCellRenderer/index.tsx

@@ -53,16 +53,15 @@ const CivicCellRenderer = ({
     }
   }, [data, externalStatementId, externalSource]);
 
-  const menuItems = links.map((linkId) => (
-    <MenuItem
-      key={linkId}
-      onClick={handleMenuClose}
-    >
-      <NewTabLink link={`https://civicdb.org/links/evidence/${linkId}`} text={linkId} />
-    </MenuItem>
-  ));
-
   if (links.length > 1) {
+    const menuItems = links.map((linkId) => (
+      <MenuItem
+        key={linkId}
+        onClick={handleMenuClose}
+      >
+        <NewTabLink link={`https://civicdb.org/links/evidence/${linkId}`} text={linkId} />
+      </MenuItem>
+    ));
     return (
       <>
         <span>{text ? `${text},` : ''}</span>
@@ -71,6 +70,8 @@ const CivicCellRenderer = ({
           style={{
             backgroundColor: 'unset',
             border: 'none',
+            padding: 0,
+            fontFamily: 'inherit',
           }}
           aria-label="Open in CIViC"
           title="Open in CIViC"

app/components/TumourSummaryEdit/index.tsx

@@ -19,8 +19,7 @@ import useConfirmDialog from '@/hooks/useConfirmDialog';
 
 import './index.scss';
 import { ReportType } from '@/context/ReportContext';
-import { MutationBurdenType } from '../../../MutationBurden/types';
-import { MicrobialType } from '../../types';
+import { MicrobialType, MutationBurdenType } from '@/common';
 
 type TumourSummaryEditProps = {
   microbial: MicrobialType[];

app/context/ReportContext/types.d.ts

@@ -53,6 +53,7 @@ type ReportType = {
   users: UserRoleType[];
   oncotreeTumourType: string;
   kbDiseaseMatch: string;
+  m1m2Score: number;
 } & RecordDefaults;
 
 type ReportContextType = {

app/views/PrintView/index.tsx

@@ -112,21 +112,21 @@ const Print = (): JSX.Element => {
               <PageBreak />
             </>
           )}
-          {template?.sections.includes('analyst-comments') && (
+          {template?.sections.includes('therapeutic-targets') && (
             <>
-              <AnalystComments report={report} isPrint loadedDispatch={dispatch} />
+              <TherapeuticTargets isPrint loadedDispatch={dispatch} />
               <PageBreak />
             </>
           )}
-          {template?.sections.includes('pathway-analysis') && (
+          {template?.sections.includes('analyst-comments') && (
             <>
-              <PathwayAnalysis report={report} isPrint loadedDispatch={dispatch} />
+              <AnalystComments report={report} isPrint loadedDispatch={dispatch} />
               <PageBreak />
             </>
           )}
-          {template?.sections.includes('therapeutic-targets') && (
+          {template?.sections.includes('pathway-analysis') && (
             <>
-              <TherapeuticTargets isPrint loadedDispatch={dispatch} />
+              <PathwayAnalysis report={report} isPrint loadedDispatch={dispatch} />
               <PageBreak />
             </>
           )}

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

@@ -23,19 +23,20 @@ import withLoading, { WithLoadingInjectedProps } from '@/hoc/WithLoading';
 import PatientEdit from '@/components/PatientEdit';
 import useConfirmDialog from '@/hooks/useConfirmDialog';
 import TumourSummaryEdit from '@/components/TumourSummaryEdit';
-import { TumourSummaryType, TmburType, MsiType } from '@/common';
+import {
+  TumourSummaryType, MicrobialType, ImmuneType, MutationBurdenType, TmburType, MsiType,
+} from '@/common';
+
 import VariantChips from './components/VariantChips';
 import VariantCounts from './components/VariantCounts';
 import {
   PatientInformationType,
   GeneVariantType,
-  MicrobialType,
 } from './types';
 import {
-  MutationBurdenType, ComparatorType,
+  ComparatorType,
 } from '../MutationBurden/types';
 import MutationSignatureType from '../MutationSignatures/types';
-import { ImmuneType } from '../Immune/types';
 
 import './index.scss';
 

app/views/ReportView/components/GenomicSummary/types.d.ts

@@ -10,13 +10,7 @@ type GeneVariantType = {
   type?: string;
 } & RecordDefaults;
 
-type MicrobialType = {
-  integrationSite: string | null;
-  species: string | null;
-} & RecordDefaults;
-
 export {
   PatientInformationType,
   GeneVariantType,
-  MicrobialType,
 };

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

@@ -7,8 +7,9 @@ import ReportContext from '@/context/ReportContext';
 import api, { ApiCallSet } from '@/services/api';
 import snackbar from '@/services/SnackbarUtils';
 import withLoading, { WithLoadingInjectedProps } from '@/hoc/WithLoading';
+import { ImmuneType } from '@/common';
 import { hlaColumnDefs, cellTypesColumnDefs } from './columnDefs';
-import { ImmuneType, HlaType } from './types';
+import { HlaType } from './types';
 
 import './index.scss';
 

app/views/ReportView/components/Immune/types.d.ts

@@ -1,12 +1,5 @@
 import { RecordDefaults } from '@/common';
 
-type ImmuneType = {
-  cellType: string | null;
-  kbCategory: string | null;
-  percentile: number | null;
-  score: number | null;
-} & RecordDefaults;
-
 type HlaType = {
   a1: string;
   a2: string;
@@ -22,6 +15,5 @@ type HlaType = {
 } & RecordDefaults;
 
 export {
-  ImmuneType,
   HlaType,
 };