fix decipher link

broadinstitute · Aug 8, 2023 · ab63a0b · ab63a0b
1 parent a09284a
commit ab63a0b
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Showing 3 changed files with 10 additions and 3 deletions.
diff --git a/ui/shared/components/panel/genes/GeneDetail.jsx b/ui/shared/components/panel/genes/GeneDetail.jsx
@@ -8,6 +8,7 @@ import { Grid, Popup, Loader, Label } from 'semantic-ui-react'
 
 import { loadGene, updateGeneNote } from 'redux/rootReducer'
 import { getGenesIsLoading, getGenesById, getUser } from 'redux/selectors'
+import { getDecipherGeneLink } from 'shared/utils/constants'
 import { SectionHeader, ColoredLabel } from '../../StyledComponents'
 import DataLoader from '../../DataLoader'
 import NoteListFieldView from '../view-fields/NoteListFieldView'
@@ -311,7 +312,7 @@ const GeneDetailContent = React.memo(({ gene, user, updateGeneNote: dispatchUpda
     { title: 'NCBI Gene', link: `http://www.ncbi.nlm.nih.gov/gene/?term=${gene.geneId}`, description: 'NCBI\'s gene information resource' },
     { title: 'GTEx Portal', link: `http://www.gtexportal.org/home/gene/${gene.geneId}`, description: 'Reference of public data for this gene' },
     { title: 'Monarch', link: `http://monarchinitiative.org/gene/ENSEMBL:${gene.geneId}`, description: 'Cross-species gene and phenotype resource' },
-    { title: 'Decipher', link: `https://decipher.sanger.ac.uk/gene/${gene.geneId}/overview/protein-genomic-info`, description: 'DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources' },
+    { title: 'Decipher', link: getDecipherGeneLink(gene), description: 'DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources' },
     { title: 'UniProt', link: `http://www.uniprot.org/uniprot?query=${gene.geneId}+AND(reviewed:true)+AND(organism_id:9606)`, description: 'Protein sequence and functional information' },
     { title: 'Geno2MP', link: `https://geno2mp.gs.washington.edu/Geno2MP/#/gene/${gene.geneSymbol}/gene/0/0/0`, description: 'Genotype to Mendelian Phenotype' },
     { title: 'gnomAD', link: `https://gnomad.broadinstitute.org/gene/${gene.geneId}?dataset=gnomad_r3`, description: 'Genome Aggregation Database' },

diff --git a/ui/shared/components/panel/variants/VariantGene.jsx b/ui/shared/components/panel/variants/VariantGene.jsx
@@ -9,7 +9,11 @@ import { getGenesById, getLocusListsByGuid, getFamiliesByGuid } from 'redux/sele
 import DataTable from 'shared/components/table/DataTable'
 import { panelAppUrl, moiToMoiInitials } from '../../../utils/panelAppUtils'
 import {
-  MISSENSE_THRESHHOLD, LOF_THRESHHOLD, PANEL_APP_CONFIDENCE_LEVEL_COLORS, PANEL_APP_CONFIDENCE_DESCRIPTION,
+  MISSENSE_THRESHHOLD,
+  LOF_THRESHHOLD,
+  PANEL_APP_CONFIDENCE_LEVEL_COLORS,
+  PANEL_APP_CONFIDENCE_DESCRIPTION,
+  getDecipherGeneLink,
 } from '../../../utils/constants'
 import { compareObjects } from '../../../utils/sortUtils'
 import { camelcaseToTitlecase } from '../../../utils/stringUtils'
@@ -589,7 +593,7 @@ export const BaseVariantGene = React.memo(({
   } else {
     summaryDetail = (
       <GeneLinks>
-        <a href={`https://decipher.sanger.ac.uk/gene/${gene.geneId}/overview/protein-genomic-info`} target="_blank" rel="noreferrer">
+        <a href={getDecipherGeneLink(gene)} target="_blank" rel="noreferrer">
           Decipher
         </a>
         &nbsp; | &nbsp;

diff --git a/ui/shared/utils/constants.js b/ui/shared/utils/constants.js
@@ -1113,6 +1113,8 @@ export const LOF_THRESHHOLD = 0.35
 
 const PRIORITIZED_GENE_MAX_RANK = 1000
 
+export const getDecipherGeneLink = ({ geneId }) => `https://www.deciphergenomics.org/gene/${geneId}/overview/protein-genomic-info`
+
 const getGeneConstraintSortScore = ({ constraints }) => {
   if (!constraints || constraints.louef === undefined) {
     return Infinity