Create gene on gene link click if does not exist (#469)

oncokb · Nov 7, 2024 · 8b4edf6 · 8b4edf6
1 parent 8708e25
commit 8b4edf6
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Showing 3 changed files with 46 additions and 11 deletions.
diff --git a/src/main/webapp/app/pages/curation/GeneListPage.tsx b/src/main/webapp/app/pages/curation/GeneListPage.tsx
@@ -3,8 +3,8 @@ import { connect } from 'app/shared/util/typed-inject';
 import { IRootStore } from 'app/stores';
 import { Col, Row } from 'reactstrap';
 import LoadingIndicator, { LoaderSize } from 'app/oncokb-commons/components/loadingIndicator/LoadingIndicator';
-import { geneNeedsReview } from 'app/shared/util/firebase/firebase-utils';
-import { Link, RouteComponentProps, generatePath } from 'react-router-dom';
+import { createGeneIfDoesNotExist, geneNeedsReview } from 'app/shared/util/firebase/firebase-utils';
+import { Link, RouteComponentProps, generatePath, useHistory } from 'react-router-dom';
 import { APP_DATETIME_FORMAT, GERMLINE_PATH, PAGE_ROUTE } from 'app/config/constants/constants';
 import OncoKBTable, { SearchColumn } from 'app/shared/table/OncoKBTable';
 import { filterByKeyword } from 'app/shared/util/utils';
@@ -22,6 +22,7 @@ const getCurationPageLink = (hugoSymbol: string, isGermline: boolean) => {
 };
 import CurationDataImportTab from 'app/components/tabs/curation-data-import-tab/CurationDataImportTab';
 import { DATA_IMPORT_TAB_ID, GENE_LIST_TABLE_ID } from 'app/config/constants/html-id';
+import { notifyError } from 'app/oncokb-commons/components/util/NotificationUtils';
 
 type GeneMetaInfo = {
   hugoSymbol: string;
@@ -33,6 +34,8 @@ type GeneMetaInfo = {
 export interface IGeneListPage extends StoreProps, RouteComponentProps {}
 
 const GeneListPage = (props: IGeneListPage) => {
+  const history = useHistory();
+
   const pathname = props.location.pathname;
   const isGermline = pathname.includes(GERMLINE_PATH);
 
@@ -67,7 +70,26 @@ const GeneListPage = (props: IGeneListPage) => {
       accessor: 'hugoSymbol',
       Header: 'Hugo Symbol',
       Cell(cell: { value: string }): any {
-        return <Link to={getCurationPageLink(cell.value, isGermline)}>{cell.value}</Link>;
+        const link = getCurationPageLink(cell.value, isGermline);
+
+        return (
+          <Link
+            to={undefined}
+            onClick={async event => {
+              event.preventDefault();
+              if (props.firebaseDb) {
+                try {
+                  await createGeneIfDoesNotExist(cell.value, isGermline, props.firebaseDb, props.createGene);
+                  history.push(link);
+                } catch (error) {
+                  notifyError(error);
+                }
+              }
+            }}
+          >
+            {cell.value}
+          </Link>
+        );
       },
       onFilter: (data: GeneMetaInfo, keyword) => (data.hugoSymbol ? filterByKeyword(data.hugoSymbol, keyword) : false),
     },
@@ -161,12 +183,14 @@ const GeneListPage = (props: IGeneListPage) => {
   );
 };
 
-const mapStoreToProps = ({ firebaseMetaStore, firebaseAppStore }: IRootStore) => ({
+const mapStoreToProps = ({ firebaseMetaStore, firebaseAppStore, firebaseGeneService }: IRootStore) => ({
+  firebaseDb: firebaseAppStore.firebaseDb,
   firebaseReady: firebaseAppStore.firebaseReady,
   firebaseInitError: firebaseAppStore.firebaseInitError,
   firebaseLoginError: firebaseAppStore.firebaseLoginError,
   addMetaListener: firebaseMetaStore.addListener,
   metaData: firebaseMetaStore.data,
+  createGene: firebaseGeneService.createGene,
 });
 
 type StoreProps = ReturnType<typeof mapStoreToProps>;

diff --git a/src/main/webapp/app/pages/curation/button/SomaticGermlineToggleButton.tsx b/src/main/webapp/app/pages/curation/button/SomaticGermlineToggleButton.tsx
@@ -1,5 +1,5 @@
 import { notifyError } from 'app/oncokb-commons/components/util/NotificationUtils';
-import { getFirebasePath } from 'app/shared/util/firebase/firebase-utils';
+import { createGeneIfDoesNotExist, getFirebasePath } from 'app/shared/util/firebase/firebase-utils';
 import { componentInject } from 'app/shared/util/typed-inject';
 import { IRootStore } from 'app/stores';
 import { get, ref } from 'firebase/database';
@@ -29,14 +29,10 @@ function SomaticGermlineToggleButton({ hugoSymbol, firebaseDb, createGene }: ISo
     if (!firebaseDb) {
       return;
     }
-    if (hugoSymbol) {
+    if (hugoSymbol && createGene) {
       // On curation page
-      const genePath = getFirebasePath(isSomatic ? 'GENE' : 'GERMLINE_GENE', hugoSymbol);
       try {
-        const snapshot = await get(ref(firebaseDb, genePath));
-        if (!snapshot.exists()) {
-          await createGene?.(hugoSymbol, !isSomatic);
-        }
+        await createGeneIfDoesNotExist(hugoSymbol, newVariantType === 'germline', firebaseDb, createGene);
       } catch (error) {
         notifyError(error);
       }

diff --git a/src/main/webapp/app/shared/util/firebase/firebase-utils.tsx b/src/main/webapp/app/shared/util/firebase/firebase-utils.tsx
@@ -29,6 +29,8 @@ import { extractPositionFromSingleNucleotideAlteration, getCancerTypeName, isUui
 import { isTxLevelPresent } from './firebase-level-utils';
 import { parseFirebaseGenePath } from './firebase-path-utils';
 import { hasReview } from './firebase-review-utils';
+import { Database, ref, get } from 'firebase/database';
+import { FirebaseGeneService } from 'app/service/firebase/firebase-gene-service';
 
 export const getValueByNestedKey = (obj: any, nestedKey = '') => {
   return nestedKey.split('/').reduce((currObj, currKey) => {
@@ -961,3 +963,16 @@ export function areCancerTypePropertiesEqual(a: string | undefined, b: string |
 export function isStringEmpty(string: string | undefined | null) {
   return string === '' || _.isNil(string);
 }
+
+export async function createGeneIfDoesNotExist(
+  hugoSymbol: string,
+  isGermline: boolean,
+  firebaseDb: Database,
+  createGene: typeof FirebaseGeneService.prototype.createGene,
+) {
+  const genePath = getFirebasePath(isGermline ? 'GERMLINE_GENE' : 'GENE', hugoSymbol);
+  const snapshot = await get(ref(firebaseDb, genePath));
+  if (!snapshot.exists()) {
+    await createGene?.(hugoSymbol, isGermline);
+  }
+}