Fix immediate deletion logic (#332)

Author: calvinlu3

src/main/webapp/app/pages/curation/collapsible/CancerTypeCollapsible.tsx

@@ -2,7 +2,7 @@ import { CancerType, Review } from 'app/shared/model/firebase/firebase.model';
 import { componentInject } from 'app/shared/util/typed-inject';
 import { getCancerTypesNameWithExclusion } from 'app/shared/util/utils';
 import { IRootStore } from 'app/stores';
-import { onValue, ref } from 'firebase/database';
+import { get, onValue, ref } from 'firebase/database';
 import { observer } from 'mobx-react';
 import React, { useEffect, useState } from 'react';
 import GeneHistoryTooltip from 'app/components/geneHistoryTooltip/GeneHistoryTooltip';
@@ -81,6 +81,11 @@ function CancerTypeCollapsible({
     return () => callbacks.forEach(callback => callback?.());
   }, [cancerTypePath, firebaseDb]);
 
+  async function handleDeleteCancerType() {
+    const snapshot = await get(ref(firebaseDb, cancerTypePath));
+    deleteSection(`${cancerTypePath}/cancerTypes`, snapshot.val(), cancerTypesReview, cancerTypesUuid);
+  }
+
   if (!cancerTypes || !cancerTypesUuid) {
     return <></>;
   }
@@ -110,7 +115,7 @@ function CancerTypeCollapsible({
             />
             <DeleteSectionButton
               sectionName={cancerTypeName}
-              deleteHandler={() => deleteSection(`${cancerTypePath}/cancerTypes`, cancerTypesReview, cancerTypesUuid)}
+              deleteHandler={handleDeleteCancerType}
               isRemovableWithoutReview={isRemovableWithoutReview}
             />
           </>

src/main/webapp/app/pages/curation/collapsible/MutationCollapsible.tsx

@@ -23,6 +23,7 @@ import { Alteration, Review } from 'app/shared/model/firebase/firebase.model';
 import DefaultTooltip from 'app/shared/tooltip/DefaultTooltip';
 import { FlattenedHistory } from 'app/shared/util/firebase/firebase-history-utils';
 import {
+  findNestedUuids,
   getFirebaseGenePath,
   getFirebaseVusPath,
   getMutationName,
@@ -32,7 +33,7 @@ import {
 import { componentInject } from 'app/shared/util/typed-inject';
 import { getExonRanges } from 'app/shared/util/utils';
 import { IRootStore } from 'app/stores';
-import { onValue, ref } from 'firebase/database';
+import { get, onValue, ref } from 'firebase/database';
 import _ from 'lodash';
 import { observer } from 'mobx-react';
 import React, { useEffect, useMemo, useState } from 'react';
@@ -170,12 +171,11 @@ const MutationCollapsible = ({
     return () => callbacks.forEach(callback => callback?.());
   }, [mutationPath, firebaseDb]);
 
-  async function handleDemoteToVus() {
-    await deleteSection(`${mutationPath}/name`, mutationNameReview, mutationUuid, true);
-    setIsConvertingToVus(false);
-    if (open) {
-      onToggle();
-    }
+  async function handleDeleteMutation(toVus = false) {
+    const snapshot = await get(ref(firebaseDb, mutationPath));
+    await deleteSection(`${mutationPath}/name`, snapshot.val(), mutationNameReview, mutationUuid, toVus);
+    if (toVus) setIsConvertingToVus(false);
+    if (open) onToggle();
   }
 
   if (!mutationUuid || !mutationName) {
@@ -247,12 +247,7 @@ const MutationCollapsible = ({
             />
             <DeleteSectionButton
               sectionName={title}
-              deleteHandler={async () => {
-                await deleteSection(`${mutationPath}/name`, mutationNameReview, mutationUuid);
-                if (open) {
-                  onToggle();
-                }
-              }}
+              deleteHandler={() => handleDeleteMutation()}
               isRemovableWithoutReview={isRemovableWithoutReview}
               tooltipProps={
                 isAssociatedWithGenomicIndicator
@@ -531,7 +526,7 @@ const MutationCollapsible = ({
           isGermline={isGermline}
           vusList={vusData}
           onCancel={() => setIsConvertingToVus(false)}
-          onConfirm={handleDemoteToVus}
+          onConfirm={() => handleDeleteMutation(true)}
           convertOptions={{
             initialAlterations: mutationName.split(',').map(alteration => alteration.trim()),
             isConverting: true,
@@ -552,6 +547,7 @@ const mapStoreToProps = ({
   drugStore,
   curationPageStore,
   firebaseGenomicIndicatorsStore,
+  firebaseMutationListStore,
 }: IRootStore) => ({
   deleteSection: firebaseGeneService.deleteSection,
   addTumor: firebaseGeneService.addTumor,
@@ -564,6 +560,7 @@ const mapStoreToProps = ({
   firebaseDb: firebaseAppStore.firebaseDb,
   annotatedAltsCache: curationPageStore.annotatedAltsCache,
   genomicIndicators: firebaseGenomicIndicatorsStore.data,
+  mutationList: firebaseMutationListStore.data,
 });
 
 type StoreProps = Partial<ReturnType<typeof mapStoreToProps>>;

src/main/webapp/app/pages/curation/collapsible/TherapyCollapsible.tsx

@@ -10,7 +10,7 @@ import { FlattenedHistory } from 'app/shared/util/firebase/firebase-history-util
 import { getTxName, isSectionRemovableWithoutReview } from 'app/shared/util/firebase/firebase-utils';
 import { componentInject } from 'app/shared/util/typed-inject';
 import { IRootStore } from 'app/stores';
-import { onValue, ref } from 'firebase/database';
+import { get, onValue, ref } from 'firebase/database';
 import { observer } from 'mobx-react';
 import React, { useEffect, useState } from 'react';
 import BadgeGroup from '../BadgeGroup';
@@ -71,6 +71,11 @@ function TherapyCollapsible({
     );
   }, [therapyPath, firebaseDb]);
 
+  async function handleDeleteTherapy() {
+    const snapshot = await get(ref(firebaseDb, therapyPath));
+    deleteSection(`${therapyPath}/name`, snapshot.val(), treatmentReview, treatmentUuid);
+  }
+
   if (!treatmentUuid || !treatmentName) {
     return <></>;
   }
@@ -96,7 +101,7 @@ function TherapyCollapsible({
             />
             <DeleteSectionButton
               sectionName={cancerTypeName}
-              deleteHandler={() => deleteSection(`${therapyPath}/name`, treatmentReview, treatmentUuid)}
+              deleteHandler={handleDeleteTherapy}
               isRemovableWithoutReview={isRemovableWithoutReview}
             />
           </>

src/main/webapp/app/service/firebase/firebase-gene-service.ts

@@ -12,9 +12,9 @@ import {
   Tumor,
 } from 'app/shared/model/firebase/firebase.model';
 import { isTxLevelPresent } from 'app/shared/util/firebase/firebase-level-utils';
-import { parseFirebaseGenePath } from 'app/shared/util/firebase/firebase-path-utils';
+import { extractArrayPath, parseFirebaseGenePath } from 'app/shared/util/firebase/firebase-path-utils';
 import { FirebaseGeneReviewService } from 'app/service/firebase/firebase-gene-review-service';
-import { getFirebaseGenePath, isSectionRemovableWithoutReview } from 'app/shared/util/firebase/firebase-utils';
+import { findNestedUuids, getFirebaseGenePath, isSectionRemovableWithoutReview } from 'app/shared/util/firebase/firebase-utils';
 import AuthStore from '../../stores/authentication.store';
 import { FirebaseRepository } from '../../stores/firebase/firebase-repository';
 import { FirebaseMetaService } from './firebase-meta-service';
@@ -24,6 +24,7 @@ import { notifyError } from 'app/oncokb-commons/components/util/NotificationUtil
 import { getErrorMessage } from 'app/oncokb-commons/components/alert/ErrorAlertUtils';
 import { FirebaseDataStore } from 'app/stores/firebase/firebase-data.store';
 import { getUpdatedReview } from 'app/shared/util/firebase/firebase-review-utils';
+import { SentryError } from 'app/config/sentry-error';
 
 export type AllLevelSummary = {
   [mutationUuid: string]: {
@@ -192,7 +193,13 @@ export class FirebaseGeneService {
     return summary;
   };
 
-  deleteSection = async (path: string, review: Review, uuid: string, isDemotedToVus = false) => {
+  deleteSection = async (
+    path: string,
+    sectionObject: Mutation | Tumor | Treatment | GenomicIndicator,
+    review: Review,
+    uuid: string,
+    isDemotedToVus = false,
+  ) => {
     const isGermline = path.toLowerCase().includes('germline');
     const name = this.authStore.fullName;
     const pathDetails = parseFirebaseGenePath(path);
@@ -211,21 +218,25 @@ export class FirebaseGeneService {
     }
 
     if (removeWithoutReview) {
-      const pathParts = path.split('/');
-      const indexToRemove = parseInt(pathParts.pop(), 10);
-      const arrayPath = pathParts.join('/');
-      return this.firebaseRepository.deleteFromArray(arrayPath, [indexToRemove]);
+      const { firebaseArrayPath, deleteIndex } = extractArrayPath(path);
+      const nestedUuids = findNestedUuids(sectionObject);
+      try {
+        await this.firebaseRepository.deleteFromArray(firebaseArrayPath, [deleteIndex]);
+        for (const id of nestedUuids) {
+          await this.firebaseMetaService.updateGeneReviewUuid(hugoSymbol, id, false, isGermline);
+        }
+      } catch (error) {
+        throw new SentryError('Failed to delete without review', { path, sectionObject, review, uuid, isDemotedToVus });
+      }
+    } else {
+      // Let the deletion be reviewed
+      try {
+        await this.firebaseRepository.update(getFirebaseGenePath(isGermline, hugoSymbol), { [`${pathFromGene}_review`]: review });
+        await this.firebaseMetaService.updateMeta(hugoSymbol, uuid, true, isGermline);
+      } catch (error) {
+        throw new SentryError('Failed to mark deletion for review', { path, sectionObject, review, uuid, isDemotedToVus });
+      }
     }
-
-    // Let the deletion be reviewed
-    return this.firebaseRepository
-      .update(getFirebaseGenePath(isGermline, hugoSymbol), {
-        [`${pathFromGene}_review`]: review,
-      })
-      .then(() => {
-        this.firebaseMetaService.updateGeneMetaContent(hugoSymbol, isGermline);
-        this.firebaseMetaService.updateGeneReviewUuid(hugoSymbol, uuid, true, isGermline);
-      });
   };
 
   createGene = async (hugoSymbol: string, isGermline: boolean, routeAfter?: string) => {

src/main/webapp/app/shared/table/GenomicIndicatorsTable.tsx

@@ -13,11 +13,12 @@ import './genomic-indicators-table.scss';
 import { DeleteSectionButton } from 'app/pages/curation/button/DeleteSectionButton';
 import DefaultBadge from '../badge/DefaultBadge';
 import { DELETED_SECTION_TOOLTIP_OVERLAY } from 'app/pages/curation/BadgeGroup';
-import { getFirebasePath, getMutationName, isSectionRemovableWithoutReview } from '../util/firebase/firebase-utils';
+import { findNestedUuids, getFirebasePath, getMutationName, isSectionRemovableWithoutReview } from '../util/firebase/firebase-utils';
 import { DANGER } from 'app/config/colors';
 import { getHexColorWithAlpha } from '../util/utils';
 import { parseFirebaseGenePath } from '../util/firebase/firebase-path-utils';
 import GenomicIndicatorsHeader from 'app/pages/curation/header/GenomicIndicatorsHeader';
+import { SentryError } from 'app/config/sentry-error';
 
 export interface IGenomicIndicatorsTableProps extends StoreProps {
   genomicIndicatorsPath: string;
@@ -32,6 +33,7 @@ const GenomicIndicatorsTable = ({
   updateReviewableContent,
   updateGeneMetaContent,
   updateGeneReviewUuid,
+  updateMeta,
   fetchGenomicIndicators,
 }: IGenomicIndicatorsTableProps) => {
   const [genomicIndicatorsLength, setGenomicIndicatorsLength] = useState<number>(0);
@@ -48,17 +50,27 @@ const GenomicIndicatorsTable = ({
     const review = new Review(name, undefined, undefined, true);
 
     if (removeWithoutReview) {
-      await deleteGenomicIndicators(genomicIndicatorsPath, [index]);
-      return await fetchGenomicIndicators(genomicIndicatorsPath);
+      const nestedUuids = findNestedUuids(genomicIndicator);
+      try {
+        await deleteGenomicIndicators(genomicIndicatorsPath, [index]);
+        for (const id of nestedUuids) {
+          await updateGeneReviewUuid(hugoSymbol, id, false, true);
+        }
+        return await fetchGenomicIndicators(genomicIndicatorsPath);
+      } catch (error) {
+        throw new SentryError('Failed to genomic indicator without review', { genomicIndicator, index });
+      }
     }
 
     // Let the deletion be reviewed
-    return update(ref(firebaseDb, `${getFirebasePath('GERMLINE_GENE', hugoSymbol)}`), {
-      [`${pathFromGene}_review`]: review,
-    }).then(() => {
-      updateGeneMetaContent(hugoSymbol, true);
-      updateGeneReviewUuid(hugoSymbol, genomicIndicator.name_uuid, true, true);
-    });
+    try {
+      await update(ref(firebaseDb, `${getFirebasePath('GERMLINE_GENE', hugoSymbol)}`), {
+        [`${pathFromGene}_review`]: review,
+      });
+      await updateMeta(hugoSymbol, genomicIndicator.name_uuid, true, true);
+    } catch (error) {
+      throw new SentryError('Failed to mark genomic indicator deletion for review', { genomicIndicator, index });
+    }
   }
 
   useEffect(() => {
@@ -308,6 +320,7 @@ const mapStoreToProps = ({
   updateGeneReviewUuid: firebaseMetaService.updateGeneReviewUuid,
   mutations: firebaseMutationListStore.data,
   fetchGenomicIndicators: firebaseGenomicIndicatorsStore.fetchData,
+  updateMeta: firebaseMetaService.updateMeta,
 });
 
 type StoreProps = Partial<ReturnType<typeof mapStoreToProps>>;

src/main/webapp/app/shared/util/firebase/firebase-review-utils.tsx

@@ -823,3 +823,16 @@ export const getUpdatedReview = (oldReview: Review, currentValue: any, newValue:
 
   return { updatedReview: oldReview, isChangeReverted };
 };
+
+export const hasReview = (review: Review) => {
+  if (review.lastReviewed === '' || !_.isEmpty(review.lastReviewed)) {
+    return true;
+  }
+  const reviewableKeys: (keyof Review)[] = ['added', 'promotedToMutation', 'removed', 'demotedToVus', 'initialUpdate'];
+  for (const key of reviewableKeys) {
+    if (review[key] === true) {
+      return true;
+    }
+  }
+  return false;
+};

src/main/webapp/app/shared/util/firebase/firebase-utils.tsx

@@ -27,6 +27,7 @@ import { replaceUrlParams } from '../url-utils';
 import { extractPositionFromSingleNucleotideAlteration, isUuid, parseAlterationName } from '../utils';
 import { isTxLevelPresent } from './firebase-level-utils';
 import { parseFirebaseGenePath } from './firebase-path-utils';
+import { hasReview } from './firebase-review-utils';
 
 export const getValueByNestedKey = (obj: any, nestedKey = '') => {
   return nestedKey.split('/').reduce((currObj, currKey) => {
@@ -784,3 +785,27 @@ export const getReviewInfo = (editor: string, action: string, updateTime?: strin
 export const getAllCommentsString = (comments: Comment[]) => {
   return comments.map(comment => comment.content).join('\n');
 };
+
+export function findNestedUuids(obj: any, uuids: string[] = []) {
+  // Base case: if the input is not an object, return
+  if (typeof obj !== 'object' || obj === null) {
+    return uuids;
+  }
+
+  // Iterate through each key in the object
+  for (const key of Object.keys(obj)) {
+    if (key.endsWith('_review') && hasReview(obj[key])) {
+      // If the key ends with "_review" and has reviewable content, add the corresponding "_uuid" key to the result array
+      const uuidKey = key.slice(0, -7) + '_uuid';
+      if (obj[uuidKey]) {
+        uuids.push(obj[uuidKey]);
+      }
+    }
+    // If the value is an object, recursively call the function
+    if (typeof obj[key] === 'object') {
+      findNestedUuids(obj[key], uuids);
+    }
+  }
+
+  return uuids;
+}