fix(variant): SKFP-850 fix NO_GENE case (#3839)

kids-first · Nov 6, 2023 · 708dcc8 · 708dcc8
1 parent dc78e4f
commit 708dcc8
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Showing 8 changed files with 53 additions and 44 deletions.
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -53,7 +53,7 @@
     "@apollo/client": "^3.5.10",
     "@dnd-kit/core": "^4.0.3",
     "@dnd-kit/sortable": "^5.1.0",
-    "@ferlab/ui": "^7.14.0",
+    "@ferlab/ui": "^7.14.2",
     "@loadable/component": "^5.15.2",
     "@react-keycloak/core": "^3.2.0",
     "@react-keycloak/web": "^3.4.0",

diff --git a/src/views/DataExploration/components/PageContent/index.tsx b/src/views/DataExploration/components/PageContent/index.tsx
@@ -88,7 +88,7 @@ const PageContent = ({
   participantMapping,
   tabId = TAB_IDS.SUMMARY,
 }: OwnProps) => {
-  const dispatch = useDispatch();
+  const dispatch = useDispatch<any>();
   const history = useHistory();
   const { savedSets } = useSavedSet();
   const { queryList, activeQuery, selectedSavedFilter, savedFilterList } =

diff --git a/src/views/VariantEntity/FerlabComponent/EntityGeneConsequence.tsx b/src/views/VariantEntity/FerlabComponent/EntityGeneConsequence.tsx
@@ -1,8 +1,10 @@
 import React from 'react';
+import { NO_GENE } from '@ferlab/ui/core/components/Consequences/Cell';
 import { ProColumnType } from '@ferlab/ui/core/components/ProTable/types';
 import { IArrangerEdge } from '@ferlab/ui/core/graphql/types';
 import { hydrateResults } from '@ferlab/ui/core/graphql/utils';
 import { EntityExpandableTableMultiple } from '@ferlab/ui/core/pages/EntityPage';
+
 import { IGeneEntity } from '../../../graphql/variants/models';
 
 import EntityGeneConsequenceSubtitle from './EntityGeneConsequenceSubtitle';
@@ -38,22 +40,24 @@ export const EntityGeneConsequences = ({
     id={id}
     loading={loading}
     tables={
-      genes?.map((gene) => ({
-        columns,
-        data: hydrateResults(gene?.node?.consequences?.hits?.edges || []),
-        subTitle: (
-          <EntityGeneConsequenceSubtitle
-            gene={gene}
-            dictionary={{
-              gene: 'Gene',
-              omim: 'Omim',
-              spliceai: 'SpliceAI',
-              gnomad_pli: 'gnomAD pLI',
-              gnomad_loeuf: 'gnomAD LOEUF',
-            }}
-          />
-        ),
-      })) || []
+      genes
+        ?.filter((gene) => gene.node.symbol !== NO_GENE)
+        .map((gene) => ({
+          columns,
+          data: hydrateResults(gene?.node?.consequences?.hits?.edges || []),
+          subTitle: (
+            <EntityGeneConsequenceSubtitle
+              gene={gene}
+              dictionary={{
+                gene: 'Gene',
+                omim: 'Omim',
+                spliceai: 'SpliceAI',
+                gnomad_pli: 'gnomAD pLI',
+                gnomad_loeuf: 'gnomAD LOEUF',
+              }}
+            />
+          ),
+        })) || []
     }
     title={title}
   />

diff --git a/src/views/VariantEntity/FerlabComponent/Pathogenecity.utils.tsx b/src/views/VariantEntity/FerlabComponent/Pathogenecity.utils.tsx
@@ -6,6 +6,7 @@ import {
 } from '@ferlab/ui/core/pages/EntityPage/type';
 import { groupRowsBySource } from '@ferlab/ui/core/pages/EntityPage/utils/pathogenicity';
 import { toKebabCase } from '@ferlab/ui/core/utils/stringUtils';
+
 import {
   IGeneCosmic,
   IGeneDdd,
@@ -92,7 +93,7 @@ export const makeUnGroupedDataRows = (genes: IArrangerEdge<IGeneEntity>[]) => {
   }
 
   return genes.map((gene) => {
-    const rowOrphanet = orphanetFromEdges(gene, gene.node.orphanet.hits.edges || []);
+    const rowOrphanet = orphanetFromEdges(gene, gene.node.orphanet?.hits?.edges || []);
     const rowOmim = omimFromEdges(gene, keepOnlyOmimWithId(gene.node.omim?.hits?.edges || []));
     const rowCosmic = cosmicFromEdges(gene, gene.node.cosmic?.hits?.edges || []);
     const rowHpo = hpoFromEdges(gene, gene.node.hpo?.hits?.edges || []);

diff --git a/src/views/VariantEntity/utils/consequences.tsx b/src/views/VariantEntity/utils/consequences.tsx
@@ -13,11 +13,12 @@ import {
 } from '@ferlab/ui/core/pages/EntityPage/utils/consequences';
 import { removeUnderscoreAndCapitalize } from '@ferlab/ui/core/utils/stringUtils';
 import { Space, Tooltip, Typography } from 'antd';
-import { IConsequenceEntity, Impact } from '../../../graphql/variants/models';
 import { capitalize } from 'lodash';
 
 import { TABLE_EMPTY_PLACE_HOLDER } from 'common/constants';
 import { getEntityConsequenceDictionary } from 'utils/translation';
+
+import { IConsequenceEntity, Impact } from '../../../graphql/variants/models';
 const { Text } = Typography;
 
 import { getPredictionScore } from '../FerlabComponent/Consequences.utils';

diff --git a/src/views/VariantEntity/utils/summary.tsx b/src/views/VariantEntity/utils/summary.tsx
@@ -1,4 +1,5 @@
 import intl from 'react-intl-universal';
+import { NO_GENE } from '@ferlab/ui/core/components/Consequences/Cell';
 import ExternalLink from '@ferlab/ui/core/components/ExternalLink';
 import { IEntitySummaryColumns } from '@ferlab/ui/core/pages/EntityPage/EntitySummary';
 import {
@@ -49,22 +50,24 @@ export const getSummaryItems = (variant?: IVariantEntity): IEntitySummaryColumns
             },
             {
               label: intl.get('screen.variants.summary.genes'),
-              value: variant?.genes?.hits?.edges?.length
-                ? variant.genes.hits.edges.map((gene) => {
-                    if (!gene?.node?.symbol) {
-                      return;
-                    }
-                    return (
-                      <ExternalLink
-                        key={gene.node.symbol}
-                        className={styles.geneExternalLink}
-                        href={`https://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=${gene.node.symbol}`}
-                      >
-                        {gene.node.symbol}
-                      </ExternalLink>
-                    );
-                  })
-                : TABLE_EMPTY_PLACE_HOLDER,
+              value:
+                variant?.genes?.hits?.edges?.length &&
+                variant.genes.hits.edges.filter((gene) => gene?.node?.symbol !== NO_GENE).length
+                  ? variant.genes.hits.edges.map((gene) => {
+                      if (!gene?.node?.symbol) {
+                        return;
+                      }
+                      return (
+                        <ExternalLink
+                          key={gene.node.symbol}
+                          className={styles.geneExternalLink}
+                          href={`https://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=${gene.node.symbol}`}
+                        >
+                          {gene.node.symbol}
+                        </ExternalLink>
+                      );
+                    })
+                  : TABLE_EMPTY_PLACE_HOLDER,
             },
             {
               label: intl.get('screen.variants.summary.omim'),

diff --git a/src/views/Variants/components/PageContent/index.tsx b/src/views/Variants/components/PageContent/index.tsx
@@ -56,7 +56,7 @@ const addTagToFilter = (filter: ISavedFilter) => ({
 });
 
 const PageContent = ({ variantMapping }: OwnProps) => {
-  const dispatch = useDispatch();
+  const dispatch = useDispatch<any>();
   const { userInfo } = useUser();
   const { savedSets } = useSavedSet();
   const { queryList, activeQuery, selectedSavedFilter, savedFilterList } =