Add Gene Name to results table

ccmbioinfo · Mar 18, 2024 · 5341001 · 5341001
1 parent 6a66d68
commit 5341001
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Showing 5 changed files with 11 additions and 1 deletion.
diff --git a/react/src/components/Table/Table.tsx b/react/src/components/Table/Table.tsx
@@ -62,7 +62,7 @@ export type FlattenedQueryResponse = Omit<IndividualResponseFields, 'info' | 'di
         'callsets' | 'info'
     > &
     CallsetInfoFields &
-    VariantResponseInfoFields & { source: string; diseases: string };
+    VariantResponseInfoFields & { source: string; diseases: string; geneName: string; };
 export interface ResultTableColumns extends FlattenedQueryResponse {
     maleCount: number;
     emptyCaseDetails: string;
@@ -142,6 +142,12 @@ const Table: React.FC<TableProps> = ({ variantData }) => {
                         disableFilters: true,
                         disableSortBy: true,
                     },
+                    {
+                        accessor: 'geneName',
+                        id: 'geneName',
+                        Header: 'Gene Name',
+                        width: getColumnWidth('Gene Name'),
+                    },
                     {
                         accessor: 'start',
                         id: 'start',

diff --git a/react/src/utils/tableHelpers.ts b/react/src/utils/tableHelpers.ts
@@ -60,6 +60,7 @@ const addAdditionalFieldsAndFormatNulls = (
     gnomadHom: results.gnomadHom || 0,
     // gnomadHet: results.gnomadHet || 0,
     maleCount: 0,
+    geneName: !!results.geneName ? results.geneName! : "Not Specified",
 });
 
 export const calculateColumnWidth = (

diff --git a/server/src/resolvers/getVariantsResolver/adapters/cmhAdapter.ts b/server/src/resolvers/getVariantsResolver/adapters/cmhAdapter.ts
@@ -283,6 +283,7 @@ export const transformCMHQueryResponse: ResultTransformer<G4RDVariantQueryResult
         ref: r.variant.ref,
         start: r.variant.start,
         chromosome: r.variant.chromosome,
+        info: r.variant.info,
       };
 
       let familyId: string = '';

diff --git a/server/src/resolvers/getVariantsResolver/adapters/g4rdAdapter.ts b/server/src/resolvers/getVariantsResolver/adapters/g4rdAdapter.ts
@@ -286,6 +286,7 @@ export const transformG4RDQueryResponse: ResultTransformer<PTVariantArray> = tim
           ref: r.variant.ref,
           start: r.variant.start,
           chromosome: r.variant.chromosome,
+          info: r.variant.info,
         };
 
         const familyId: string = familyIds[individualId];

diff --git a/server/src/resolvers/getVariantsResolver/adapters/remoteTestNodeAdapter.ts b/server/src/resolvers/getVariantsResolver/adapters/remoteTestNodeAdapter.ts
@@ -163,6 +163,7 @@ const transformStagerQueryResponse: ResultTransformer<StagerVariantQueryPayload[
           ad: g.alt_depths,
           burder: g.burden,
           zygosity: g.zygosity,
+          geneName: r.gene,
         },
       })),
       end: r.position,