oncokb · jfkonecn · Apr 30, 2024
diff --git a/src/main/webapp/app/pages/curation/collapsible/ReviewCollapsible.tsx b/src/main/webapp/app/pages/curation/collapsible/ReviewCollapsible.tsx
@@ -22,6 +22,8 @@ import { CollapsibleColorProps, CollapsibleDisplayProps } from './BaseCollapsibl
 import { getReviewInfo } from 'app/shared/util/firebase/firebase-utils';
 import { notifyError } from 'app/oncokb-commons/components/util/NotificationUtils';
 import DiffViewer, { FirebaseContent } from 'app/components/diff-viewer/DiffViewer';
+import { FirebaseGeneReviewService } from 'app/service/firebase/firebase-gene-review-service';
+import { DrugCollection, Gene } from 'app/shared/model/firebase/firebase.model';
 
 export enum ReviewType {
   CREATE,
@@ -62,13 +64,16 @@ const ReviewCollapsibleBootstrapClass = {
 };
 
 export interface IReviewCollapsibleProps {
+  drugListRef: DrugCollection;
+  entrezGeneId: number;
+  gene: Gene;
   hugoSymbol: string;
   baseReviewLevel: BaseReviewLevel;
   isGermline: boolean;
   firebase: FirebaseContent;
   parentDelete?: (reviewlLevelId: string, action: ActionType, isPending?: boolean) => void;
   rootDelete?: (isPending?: boolean) => void;
-  handleAccept: (hugoSymbol: string, reviewLevels: ReviewLevel[], isGermline: boolean, isAcceptAll?: boolean) => Promise<void>;
+  handleAccept: FirebaseGeneReviewService['acceptChanges'];
   handleReject: (hugoSymbol: string, reviewLevels: ReviewLevel[], isGermline: boolean) => Promise<void>;
   handleCreateAction: (hugoSymbol: string, reviewLevel: ReviewLevel, isGermline: boolean, action: ActionType) => Promise<void>;
   disableActions?: boolean;
@@ -87,6 +92,9 @@ export const ReviewCollapsible = ({
   firebase,
   disableActions = false,
   isRoot = false,
+  drugListRef,
+  entrezGeneId,
+  gene,
 }: IReviewCollapsibleProps) => {
   const [rootReview, setRootReview] = useState<BaseReviewLevel>(baseReviewLevel);
   const [reviewChildren, setReviewChildren] = useState<BaseReviewLevel[]>([]);
@@ -193,7 +201,7 @@ export const ReviewCollapsible = ({
     // After marking collapsible as pending, it will be removed from the view. Now we need to save to firebase
     try {
       if (action === ActionType.ACCEPT) {
-        await handleAccept(hugoSymbol, getReviewLevelsForActions(), isGermline);
+        await handleAccept({ hugoSymbol, reviewLevels: getReviewLevelsForActions(), isGermline, drugListRef, entrezGeneId, gene });
       } else if (action === ActionType.REJECT) {
         await handleReject(hugoSymbol, getReviewLevelsForActions(), isGermline);
       }
@@ -363,6 +371,9 @@ export const ReviewCollapsible = ({
             handleCreateAction={handleCreateAction}
             parentDelete={deleteHandlerForChild}
             disableActions={disableActions}
+            gene={gene}
+            entrezGeneId={entrezGeneId}
+            drugListRef={drugListRef}
             firebase={{
               path: getGenePathFromValuePath(hugoSymbol, childReview.valuePath, isGermline),
               db: firebase?.db,

diff --git a/src/main/webapp/app/pages/curation/review/ReviewPage.tsx b/src/main/webapp/app/pages/curation/review/ReviewPage.tsx
@@ -12,7 +12,7 @@ import { getSectionClassName } from 'app/shared/util/utils';
 import { IRootStore } from 'app/stores';
 import { get, ref } from 'firebase/database';
 import { observer } from 'mobx-react';
-import React, { useEffect, useState } from 'react';
+import React, { useEffect, useMemo, useState } from 'react';
 import { Alert, Col, FormGroup, Input, Label, Row } from 'reactstrap';
 import { RouteComponentProps } from 'react-router-dom';
 import { useMatchGeneEntity } from 'app/hooks/useMatchGeneEntity';
@@ -23,8 +23,12 @@ import _ from 'lodash';
 import { ReviewCollapsible } from '../collapsible/ReviewCollapsible';
 import { notifyError } from 'app/oncokb-commons/components/util/NotificationUtils';
 import { AsyncSaveButton } from 'app/shared/button/AsyncSaveButton';
+import { DrugCollection, Gene, MetaReview } from 'app/shared/model/firebase/firebase.model';
+import { IGene } from 'app/shared/model/gene.model';
 
-interface IReviewPageProps extends StoreProps, RouteComponentProps<{ hugoSymbol: string }> {}
+interface IReviewPageProps extends StoreProps, RouteComponentProps<{ hugoSymbol: string }> {
+  geneEntity: IGene;
+}
 
 const ReviewPage: React.FunctionComponent<IReviewPageProps> = (props: IReviewPageProps) => {
   const pathname = props.location.pathname;
@@ -36,8 +40,8 @@ const ReviewPage: React.FunctionComponent<IReviewPageProps> = (props: IReviewPag
   const firebaseGenePath = getFirebaseGenePath(isGermline, hugoSymbol);
   const firebaseMetaReviewPath = `${getFirebaseMetaGenePath(isGermline, hugoSymbol)}/review`;
 
-  const [geneData, setGeneData] = useState(null);
-  const [metaReview, setMetaReview] = useState(null);
+  const [geneData, setGeneData] = useState<Gene | null>(null);
+  const [metaReview, setMetaReview] = useState<MetaReview | null>(null);
 
   const [isReviewFinished, setIsReviewFinished] = useState(false);
 
@@ -47,6 +51,11 @@ const ReviewPage: React.FunctionComponent<IReviewPageProps> = (props: IReviewPag
   const [editorsToAcceptChangesFrom, setEditorsToAcceptChangesFrom] = useState<string[]>([]);
   const [isAcceptingAll, setIsAcceptingAll] = useState(false);
 
+  const drugListRef: DrugCollection = useMemo(() => {
+    const group = _.mapValues(_.groupBy(props.drugList, 'uuid'), x => x[0]);
+    return group as DrugCollection;
+  }, [props.drugList]);
+
   const fetchFirebaseData = () => {
     // Fetch the data when the user enters review mode. We don't use a listener
     // because there shouldn't be another user editing the gene when it is being reviewed.
@@ -99,7 +108,15 @@ const ReviewPage: React.FunctionComponent<IReviewPageProps> = (props: IReviewPag
     }
     try {
       setIsAcceptingAll(true);
-      await props.acceptReviewChangeHandler(hugoSymbol, reviewLevels, isGermline, true);
+      await props.acceptReviewChangeHandler({
+        hugoSymbol,
+        reviewLevels,
+        isGermline,
+        isAcceptAll: true,
+        gene: geneData,
+        entrezGeneId: props.geneEntity.entrezGeneId,
+        drugListRef,
+      });
       fetchFirebaseData();
     } catch (error) {
       notifyError(error);
@@ -180,6 +197,9 @@ const ReviewPage: React.FunctionComponent<IReviewPageProps> = (props: IReviewPag
         <Row>
           <Col>
             <ReviewCollapsible
+              gene={geneData}
+              entrezGeneId={geneEntity.entrezGeneId}
+              drugListRef={drugListRef}
               hugoSymbol={hugoSymbol}
               isGermline={isGermline}
               baseReviewLevel={rootReview}

diff --git a/src/main/webapp/app/service/firebase/firebase-gene-review-service.spec.ts b/src/main/webapp/app/service/firebase/firebase-gene-review-service.spec.ts
@@ -11,6 +11,8 @@ import { ReviewLevel } from 'app/shared/util/firebase/firebase-review-utils';
 import { ReviewAction } from 'app/config/constants/firebase';
 import _ from 'lodash';
 import { ActionType } from 'app/pages/curation/collapsible/ReviewCollapsible';
+import { EvidenceApi } from 'app/shared/api/manual/evidence-api';
+import { createMockGene, createMockMutation } from 'app/shared/util/core-submission/core-submission.mocks';
 
 describe('Firebase Gene Review Service', () => {
   const DEFAULT_USERNAME = 'Test User';
@@ -20,6 +22,7 @@ describe('Firebase Gene Review Service', () => {
   const mockMetaService = mock<FirebaseMetaService>();
   const mockHistoryService = mock<FirebaseHistoryService>();
   const mockVusService = mock<FirebaseVusService>();
+  const mockEvidenceClient = mock<EvidenceApi>();
   let firebaseGeneReviewService: FirebaseGeneReviewService;
 
   beforeEach(() => {
@@ -34,6 +37,7 @@ describe('Firebase Gene Review Service', () => {
       mockMetaService,
       mockHistoryService,
       mockVusService,
+      mockEvidenceClient,
     );
     jest.useFakeTimers().setSystemTime(DEFAULT_DATE);
   });
@@ -117,7 +121,14 @@ describe('Firebase Gene Review Service', () => {
         },
       });
 
-      await firebaseGeneReviewService.acceptChanges(hugoSymbol, [reviewLevel], false);
+      await firebaseGeneReviewService.acceptChanges({
+        hugoSymbol,
+        reviewLevels: [reviewLevel],
+        isGermline: false,
+        gene,
+        drugListRef: {},
+        entrezGeneId: 0,
+      });
 
       expect(mockHistoryService.addHistory).toHaveBeenCalled();
       // We expect the lastReviewed to be cleared when accepting changes
@@ -154,7 +165,17 @@ describe('Firebase Gene Review Service', () => {
         },
       });
 
-      await firebaseGeneReviewService.acceptChanges(hugoSymbol, [reviewLevel], false);
+      await firebaseGeneReviewService.acceptChanges({
+        hugoSymbol,
+        reviewLevels: [reviewLevel],
+        isGermline: false,
+        gene: createMockGene({
+          name: hugoSymbol,
+          mutations: [createMockMutation()],
+        }),
+        drugListRef: {},
+        entrezGeneId: 0,
+      });
 
       expect(mockHistoryService.addHistory).toHaveBeenCalled();
       expect(mockFirebaseRepository.deleteFromArray).toHaveBeenCalledWith('Genes/BRAF/mutations', [0]);
@@ -186,7 +207,17 @@ describe('Firebase Gene Review Service', () => {
         },
       });
 
-      await firebaseGeneReviewService.acceptChanges(hugoSymbol, [reviewLevel], false);
+      await firebaseGeneReviewService.acceptChanges({
+        hugoSymbol,
+        reviewLevels: [reviewLevel],
+        isGermline: false,
+        gene: createMockGene({
+          name: hugoSymbol,
+          mutations: [createMockMutation()],
+        }),
+        drugListRef: {},
+        entrezGeneId: 0,
+      });
 
       expect(mockHistoryService.addHistory).toHaveBeenCalled();
       expect(mockFirebaseRepository.deleteFromArray).toHaveBeenCalledWith('Genes/BRAF/mutations', [0]);
@@ -218,8 +249,18 @@ describe('Firebase Gene Review Service', () => {
         },
       });
 
-      // An entity is created once all its changes have been accepted or rejected.
       await firebaseGeneReviewService.handleCreateAction(hugoSymbol, reviewLevel, false, ActionType.ACCEPT);
+      await firebaseGeneReviewService.acceptChanges({
+        hugoSymbol,
+        reviewLevels: [reviewLevel],
+        isGermline: false,
+        gene: createMockGene({
+          name: hugoSymbol,
+          mutations: [createMockMutation()],
+        }),
+        drugListRef: {},
+        entrezGeneId: 0,
+      });
 
       const expectedMutation = _.cloneDeep(mutation);
       delete expectedMutation.name_review.added;

diff --git a/src/main/webapp/app/service/firebase/firebase-gene-review-service.ts b/src/main/webapp/app/service/firebase/firebase-gene-review-service.ts
@@ -4,7 +4,7 @@ import { FirebaseMetaService } from 'app/service/firebase/firebase-meta-service'
 import { AuthStore } from 'app/stores';
 import { FirebaseRepository } from 'app/stores/firebase/firebase-repository';
 import _ from 'lodash';
-import { Review } from '../../shared/model/firebase/firebase.model';
+import { DrugCollection, Gene, Review } from '../../shared/model/firebase/firebase.model';
 import { buildHistoryFromReviews } from '../../shared/util/firebase/firebase-history-utils';
 import { extractArrayPath, parseFirebaseGenePath } from '../../shared/util/firebase/firebase-path-utils';
 import {
@@ -23,26 +23,31 @@ import { FirebaseVusService } from './firebase-vus-service';
 import { SentryError } from 'app/config/sentry-error';
 import { ActionType } from 'app/pages/curation/collapsible/ReviewCollapsible';
 import { GERMLINE_PATH } from 'app/config/constants/constants';
+import { getEvidence, pathToGetEvidenceArgs } from 'app/shared/util/core-submission/core-submission';
+import { EvidenceApi } from 'app/shared/api/manual/evidence-api';
 
 export class FirebaseGeneReviewService {
   firebaseRepository: FirebaseRepository;
   authStore: AuthStore;
   firebaseMetaService: FirebaseMetaService;
   firebaseHistoryService: FirebaseHistoryService;
   firebaseVusService: FirebaseVusService;
+  evidenceClient: EvidenceApi;
 
   constructor(
     firebaseRepository: FirebaseRepository,
     authStore: AuthStore,
     firebaseMetaService: FirebaseMetaService,
     firebaseHistoryService: FirebaseHistoryService,
     firebaseVusService: FirebaseVusService,
+    evidenceClient: EvidenceApi,
   ) {
     this.firebaseRepository = firebaseRepository;
     this.authStore = authStore;
     this.firebaseMetaService = firebaseMetaService;
     this.firebaseHistoryService = firebaseHistoryService;
     this.firebaseVusService = firebaseVusService;
+    this.evidenceClient = evidenceClient;
   }
 
   updateReviewableContent = async (
@@ -84,10 +89,62 @@ export class FirebaseGeneReviewService {
     }
   };
 
-  acceptChanges = async (hugoSymbol: string, reviewLevels: ReviewLevel[], isGermline: boolean, isAcceptAll = false) => {
+  acceptChanges = async ({
+    gene,
+    hugoSymbol,
+    reviewLevels,
+    isGermline,
+    isAcceptAll = false,
+    drugListRef,
+    entrezGeneId,
+  }: {
+    gene: Gene;
+    hugoSymbol: string;
+    reviewLevels: ReviewLevel[];
+    isGermline: boolean;
+    isAcceptAll?: boolean;
+    drugListRef: DrugCollection;
+    entrezGeneId: number;
+  }) => {
     const geneFirebasePath = getFirebaseGenePath(isGermline, hugoSymbol);
     const vusFirebasePath = getFirebaseVusPath(isGermline, hugoSymbol);
 
+    let evidences: ReturnType<typeof getEvidence> = {};
+    let hasEvidences = false;
+    try {
+      for (const reviewLevel of reviewLevels) {
+        if (!(isCreateReview(reviewLevel) && isAcceptAll)) {
+          const args = pathToGetEvidenceArgs({
+            gene,
+            valuePath: reviewLevel.valuePath,
+            updateTime: new Date().getTime(),
+            drugListRef,
+            entrezGeneId,
+          });
+          if (args) {
+            evidences = {
+              ...getEvidence(args),
+            };
+            hasEvidences = true;
+          }
+        }
+      }
+    } catch (error) {
+      throw new SentryError('Failed to create evidences when accepting changes in review mode', { hugoSymbol, reviewLevels, isGermline });
+    }
+
+    try {
+      if (hasEvidences) {
+        await this.evidenceClient.submitEvidences(evidences);
+      }
+    } catch (error) {
+      throw new SentryError('Failed to submit evidences to core when accepting changes in review mode', {
+        hugoSymbol,
+        reviewLevels,
+        isGermline,
+      });
+    }
+
     const reviewHistory = buildHistoryFromReviews(this.authStore.fullName, reviewLevels);
     try {
       await this.firebaseHistoryService.addHistory(hugoSymbol, reviewHistory, isGermline);

diff --git a/src/main/webapp/app/shared/api/clients.ts b/src/main/webapp/app/shared/api/clients.ts
@@ -11,6 +11,7 @@ import {
   CancerTypeResourceApi,
   ArticleResourceApi,
 } from './generated/curation/api';
+import { EvidenceApi } from './manual/evidence-api';
 
 export const fdaSubmissionClient = new FdaSubmissionResourceApi(null, '', axiosInstance);
 export const geneClient = new GeneResourceApi(null, '', axiosInstance);
@@ -22,3 +23,5 @@ export const flagClient = new FlagResourceApi(null, '', axiosInstance);
 export const associationClient = new AssociationResourceApi(null, '', axiosInstance);
 export const cancerTypeClient = new CancerTypeResourceApi(null, '', axiosInstance);
 export const articleClient = new ArticleResourceApi(null, '', axiosInstance);
+
+export const evidenceClient = new EvidenceApi(null, '', axiosInstance);