feat(variant): SKFP-772 variant facet and column

kids-first · Sep 25, 2023 · 127cbdf · 127cbdf
1 parent e6a1187
commit 127cbdf
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Showing 5 changed files with 111 additions and 11 deletions.
diff --git a/src/components/uiKit/FilterList/CustomFilterSelector.tsx b/src/components/uiKit/FilterList/CustomFilterSelector.tsx
@@ -1,14 +1,16 @@
+import { useEffect } from 'react';
 import FilterSelector, {
   FilterSelectorProps,
 } from '@ferlab/ui/core/components/filters/FilterSelector';
 import useQueryBuilderState from '@ferlab/ui/core/components/QueryBuilder/utils/useQueryBuilderState';
 import { resolveSyntheticSqon } from '@ferlab/ui/core/data/sqon/utils';
+import { IExtendedMappingResults } from '@ferlab/ui/core/graphql/types';
 import { Spin } from 'antd';
-import { useEffect } from 'react';
-import useGetAggregations from 'hooks/graphql/useGetAggregations';
 import { AGGREGATION_QUERY } from 'graphql/queries';
+
+import useGetAggregations from 'hooks/graphql/useGetAggregations';
+
 import { TCustomFilterMapper } from '.';
-import { IExtendedMappingResults } from '@ferlab/ui/core/graphql/types';
 
 type OwnProps = FilterSelectorProps & {
   index: string;

diff --git a/src/components/uiKit/FilterList/index.tsx b/src/components/uiKit/FilterList/index.tsx
@@ -1,14 +1,15 @@
 import { useState } from 'react';
-import { Button, Layout, Space, Spin, Typography } from 'antd';
-import CustomFilterContainer from './CustomFilterContainer';
 import intl from 'react-intl-universal';
-import { FilterGroup, FilterInfo } from './types';
 import { ISqonGroupFilter, ISyntheticSqon } from '@ferlab/ui/core/data/sqon/types';
+import { IExtendedMappingResults } from '@ferlab/ui/core/graphql/types';
+import { Button, Layout, Space, Spin, Typography } from 'antd';
 import cx from 'classnames';
+import { isEmpty } from 'lodash';
 
 import styles from 'components/uiKit/FilterList/Filters.module.scss';
-import { isEmpty } from 'lodash';
-import { IExtendedMappingResults } from '@ferlab/ui/core/graphql/types';
+
+import CustomFilterContainer from './CustomFilterContainer';
+import { FilterGroup, FilterInfo } from './types';
 
 export type TCustomFilterMapper = (filters: ISqonGroupFilter) => ISyntheticSqon;
 
@@ -31,7 +32,7 @@ const isAllFacetOpen = (filterInfo: FilterInfo) => {
 };
 
 const concatAllFacets = (filterInfo: FilterInfo) => {
-  let allFacets: any[] = [];
+  const allFacets: any[] = [];
   filterInfo.groups.forEach(({ facets }) => allFacets.push(...facets));
   return allFacets;
 };

diff --git a/src/locales/en.ts b/src/locales/en.ts
@@ -765,6 +765,11 @@ const en = {
       },
       title: 'Variants Exploration',
       table: {
+        mostDeleteriousConsequence: {
+          title: 'Most Deleterious Consequence',
+          tooltip: 'Functional consequences of genetic variations annotated using VEP',
+        },
+        // TODO remove when new variant ETL will be used
         consequences: {
           title: 'Consequences',
           tooltip: 'Functional consequences of genetic variations annotated using VEP',
@@ -1130,6 +1135,8 @@ const en = {
     },
     studies: {
       study_code: 'Study Code',
+      zygosity: 'Zygosity',
+      transmission: 'Transmission',
     },
     is_proband: 'Proband',
     study_id: 'Study Code',
@@ -1212,6 +1219,28 @@ const en = {
       },
     },
     genes: {
+      consequences: {
+        consequence: 'Consequence',
+        vep_impact: 'VEP',
+        predictions: {
+          cadd_score: 'CADD (Raw)',
+          cadd_phred: 'CADD (Phred)',
+          dann_score: 'DANN',
+          fathmm_pred: 'FATHMM',
+          lrt_pred: 'LRT',
+          polyphen2_hvar_pred: 'PolyPhen-2 HVAR',
+          revel_score: 'REVEL',
+          sift_pred: 'SIFT',
+        },
+      },
+      biotype: 'Gene Type',
+      gnomad: {
+        pli: 'gnomAD pLI',
+        loeuf: 'gnomAD LOEUF',
+      },
+      spliceai: {
+        ds: 'SpliceAI',
+      },
       hpo: {
         hpo_term_label: 'HPO',
       },
@@ -1231,6 +1260,28 @@ const en = {
     clinvar: {
       clin_sig: 'ClinVar',
     },
+    external_frequencies: {
+      gnomad_genomes_2_1_1: {
+        af: 'gnomAD Genome 2.1.1',
+      },
+      gnomad_genomes_3: {
+        af: 'gnomAD Genome 3.1.2',
+      },
+      gnomad_exomes_2_1_1: {
+        af: 'gnomAD Exome 2.1.1',
+      },
+      topmed_bravo: {
+        af: 'TopMed',
+      },
+      thousand_genomes: {
+        af: '1000 Genomes',
+      },
+    },
+    internal_frequencies: {
+      total: {
+        af: 'KF Allele Frequency',
+      },
+    },
     frequencies: {
       internal: {
         upper_bound_kf: { af: 'KF Allele Frequency' },

diff --git a/src/utils/translation.ts b/src/utils/translation.ts
@@ -254,6 +254,8 @@ export const getFacetsDictionary = () => ({
   },
   studies: {
     study_code: 'Study Code',
+    zygosity: 'Zygosity',
+    transmission: 'Transmission',
   },
   start: 'Position',
   acl: 'ACL',
@@ -302,6 +304,28 @@ export const getFacetsDictionary = () => ({
     },
   },
   genes: {
+    consequences: {
+      consequence: 'Consequence',
+      vep_impact: 'VEP',
+      predictions: {
+        cadd_score: 'CADD (Raw)',
+        cadd_phred: 'CADD (Phred)',
+        dann_score: 'DANN',
+        fathmm_pred: 'FATHMM',
+        lrt_pred: 'LRT',
+        polyphen2_hvar_pred: 'PolyPhen-2 HVAR',
+        revel_score: 'REVEL',
+        sift_pred: 'SIFT',
+      },
+    },
+    biotype: 'Gene Type',
+    gnomad: {
+      pli: 'gnomAD pLI',
+      loeuf: 'gnomAD LOEUF',
+    },
+    spliceai: {
+      ds: 'SpliceAI',
+    },
     hpo: {
       hpo_term_label: 'HPO',
     },
@@ -318,6 +342,28 @@ export const getFacetsDictionary = () => ({
       tumour_types_germline: 'COSMIC',
     },
   },
+  external_frequencies: {
+    gnomad_genomes_2_1_1: {
+      af: 'gnomAD Genome 2.1.1',
+    },
+    gnomad_genomes_3: {
+      af: 'gnomAD Genome 3.1.2',
+    },
+    gnomad_exomes_2_1_1: {
+      af: 'gnomAD Exome 2.1.1',
+    },
+    topmed_bravo: {
+      af: 'TopMed',
+    },
+    thousand_genomes: {
+      af: '1000 Genomes',
+    },
+  },
+  internal_frequencies: {
+    total: {
+      af: 'KF Allele Frequency',
+    },
+  },
   frequencies: {
     internal: {
       upper_bound_kf: {

diff --git a/src/views/Variants2/components/PageContent/VariantsTable/index.tsx b/src/views/Variants2/components/PageContent/VariantsTable/index.tsx
@@ -107,9 +107,9 @@ const defaultColumns: ProColumnType[] = [
   },
   {
     key: 'consequences',
-    title: intl.get('screen.variants.table.consequences.title'),
+    title: intl.get('screen.variants.table.mostDeleteriousConsequence.title'),
     dataIndex: 'genes',
-    tooltip: intl.get('screen.variants.table.consequences.tooltip'),
+    tooltip: intl.get('screen.variants.table.mostDeleteriousConsequence.tooltip'),
     render: (genes: IArrangerResultsTree<IGeneEntity>) => {
       const geneWithPickedConsequence = genes?.hits?.edges?.find((e) =>
         (e.node.consequences || [])?.hits?.edges?.some((e) => e.node?.picked),