Review no longer removes data for core submission

oncokb · Sep 17, 2024 · 49c04b0 · 49c04b0
1 parent 4204647
commit 49c04b0
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Showing 7 changed files with 88 additions and 31 deletions.
diff --git a/src/main/webapp/app/pages/curation/review/ReviewPage.tsx b/src/main/webapp/app/pages/curation/review/ReviewPage.tsx
@@ -23,14 +23,10 @@ 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';
-import { FB_COLLECTION } from 'app/config/constants/firebase';
+import { Gene, MetaReview } from 'app/shared/model/firebase/firebase.model';
 import { SentryError } from 'app/config/sentry-error';
 
-interface IReviewPageProps extends StoreProps, RouteComponentProps<{ hugoSymbol: string }> {
-  geneEntity: IGene;
-}
+interface IReviewPageProps extends StoreProps, RouteComponentProps<{ hugoSymbol: string }> {}
 
 const ReviewPage: React.FunctionComponent<IReviewPageProps> = (props: IReviewPageProps) => {
   const pathname = props.location.pathname;
@@ -125,7 +121,7 @@ const ReviewPage: React.FunctionComponent<IReviewPageProps> = (props: IReviewPag
         isGermline,
         isAcceptAll: true,
         gene: geneData,
-        entrezGeneId: props.geneEntity.entrezGeneId,
+        entrezGeneId: geneEntity?.entrezGeneId as number,
         drugListRef,
       });
       fetchFirebaseData();

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
@@ -138,7 +138,7 @@ export class FirebaseGeneReviewService {
               this.evidenceClient.deleteEvidences(deleteEvidencesPayload);
             }
           } else if (isGeneTypeChange(reviewLevel.valuePath)) {
-            geneTypePayload = createGeneTypePayload(gene);
+            geneTypePayload = createGeneTypePayload(gene, reviewLevel.valuePath);
           } else {
             const args = pathToGetEvidenceArgs({
               gene,

diff --git a/src/main/webapp/app/shared/util/core-evidence-submission/core-evidence-submission.spec.ts b/src/main/webapp/app/shared/util/core-evidence-submission/core-evidence-submission.spec.ts
@@ -462,6 +462,11 @@ describe('getEvidence to submit to core', () => {
                       lastReviewed: 'Prognostic Summary Last Reviewed',
                       updateTime: getTimeFromDateString('2002-01-01'),
                     }),
+                    summary: 'Summary',
+                    summary_review: createMockReview({
+                      lastReviewed: 'Summary Last Reviewed',
+                      updateTime: getTimeFromDateString('2002-01-01'),
+                    }),
                   }),
                 ],
               }),
@@ -480,7 +485,7 @@ describe('getEvidence to submit to core', () => {
               },
             ],
             evidenceType: EvidenceEvidenceTypeEnum.PrognosticSummary,
-            description: 'Prognostic Summary Last Reviewed',
+            description: 'Prognostic Summary',
             gene: {
               entrezGeneId: baseArgs.entrezGeneId,
               hugoSymbol,
@@ -618,7 +623,7 @@ describe('getEvidence to submit to core', () => {
               },
             ],
             evidenceType: EvidenceEvidenceTypeEnum.Oncogenic,
-            knownEffect: FIREBASE_ONCOGENICITY.YES,
+            knownEffect: FIREBASE_ONCOGENICITY.LIKELY,
             gene: {
               entrezGeneId: baseArgs.entrezGeneId,
               hugoSymbol,
@@ -914,14 +919,19 @@ describe('getEvidence to submit to core', () => {
                             name: '76c75f3b-364a-418c-8661-48768fb0742a',
                             description: 'TI IS',
                             fdaLevel: FDA_LEVELS.LEVEL_FDA1,
-                            level: TX_LEVELS.LEVEL_1,
+                            level: TX_LEVELS.LEVEL_2,
                             level_review: createMockReview({
-                              lastReviewed: TX_LEVELS.LEVEL_2,
+                              lastReviewed: TX_LEVELS.LEVEL_1,
                               updatedBy: 'John Doe',
                               updateTime: getTimeFromDateString('2001-01-01'),
                             }),
                             propagationLiquid: TX_LEVELS.LEVEL_4,
                             propagation: TX_LEVELS.LEVEL_2,
+                            propagation_review: createMockReview({
+                              lastReviewed: TX_LEVELS.LEVEL_4,
+                              updatedBy: 'John Doe',
+                              updateTime: getTimeFromDateString('2001-01-01'),
+                            }),
                           }),
                         ],
                       }),
@@ -1018,6 +1028,11 @@ describe('getEvidence to submit to core', () => {
           valuePath: 'mutations/0/tumors/0/summary',
           gene: createMockGene({
             name: hugoSymbol,
+            summary: '',
+            summary_review: createMockReview({
+              updateTime: getTimeFromDateString('2004-01-01'),
+              lastReviewed: 'Ignore summary',
+            }),
             mutations: [
               createMockMutation({
                 tumors: [
@@ -1046,7 +1061,7 @@ describe('getEvidence to submit to core', () => {
               },
             ],
             evidenceType: EvidenceEvidenceTypeEnum.TumorTypeSummary,
-            description: 'Tumor Type Summary Old',
+            description: 'Tumor Type Summary',
             gene: { entrezGeneId: baseArgs.entrezGeneId, hugoSymbol },
             lastEdit: getTimeFromDateString('2004-01-01').toString(),
           },

diff --git a/src/main/webapp/app/shared/util/core-evidence-submission/core-evidence-submission.ts b/src/main/webapp/app/shared/util/core-evidence-submission/core-evidence-submission.ts
@@ -42,7 +42,7 @@ export function pathToGetEvidenceArgs({
 }: {
   valuePath: string;
 } & Pick<GetEvidenceArgs, 'gene' | 'updateTime' | 'drugListRef' | 'entrezGeneId'>): GetEvidenceArgs | undefined {
-  const gene = useLastReviewedOnly(originalGene);
+  const gene = useLastReviewedOnly(originalGene, valuePath);
   if (gene === undefined) {
     return undefined;
   }

diff --git a/src/main/webapp/app/shared/util/core-gene-type-submission/core-gene-type-submission.spec.ts b/src/main/webapp/app/shared/util/core-gene-type-submission/core-gene-type-submission.spec.ts
@@ -3,9 +3,15 @@ import { createGeneTypePayload } from './core-gene-type-submission';
 import { GENE_TYPE } from 'app/config/constants/firebase';
 
 describe('getGeneType', () => {
-  const tests: [Parameters<typeof createGeneTypePayload>[0], Required<ReturnType<typeof createGeneTypePayload>>][] = [
+  type CreateGeneTypePayloadParameters = Parameters<typeof createGeneTypePayload>;
+  const tests: [
+    CreateGeneTypePayloadParameters[0],
+    CreateGeneTypePayloadParameters[1],
+    Required<ReturnType<typeof createGeneTypePayload>>,
+  ][] = [
     [
       { name: 'name', type: { ocg: GENE_TYPE.ONCOGENE, tsg: GENE_TYPE.TUMOR_SUPPRESSOR } },
+      'type/ocg',
       {
         hugoSymbol: 'name',
         tsg: true,
@@ -22,28 +28,55 @@ describe('getGeneType', () => {
           tsg_review: { lastReviewed: '', updatedBy: '', updateTime: 0 },
         },
       },
+      'type/ocg',
       {
         hugoSymbol: 'name',
         tsg: false,
-        oncogene: false,
+        oncogene: true,
       },
     ],
     [
       {
         name: 'name',
         type: { ocg: GENE_TYPE.ONCOGENE, tsg: '', tsg_review: { lastReviewed: GENE_TYPE.TUMOR_SUPPRESSOR, updatedBy: '', updateTime: 0 } },
       },
+      'type/ocg',
       {
         hugoSymbol: 'name',
         tsg: true,
         oncogene: true,
       },
     ],
+    [
+      {
+        name: 'name',
+        type: { ocg: GENE_TYPE.ONCOGENE, tsg: '', tsg_review: { lastReviewed: GENE_TYPE.TUMOR_SUPPRESSOR, updatedBy: '', updateTime: 0 } },
+      },
+      'type/tsg',
+      {
+        hugoSymbol: 'name',
+        tsg: false,
+        oncogene: true,
+      },
+    ],
+    [
+      {
+        name: 'name',
+        type: { ocg: '', ocg_review: { lastReviewed: GENE_TYPE.ONCOGENE, updatedBy: '', updateTime: 0 }, tsg: GENE_TYPE.TUMOR_SUPPRESSOR },
+      },
+      'type/ocg',
+      {
+        hugoSymbol: 'name',
+        tsg: true,
+        oncogene: false,
+      },
+    ],
     [
       {
         name: 'name',
         type: { ocg: '', ocg_review: { lastReviewed: GENE_TYPE.ONCOGENE, updatedBy: '', updateTime: 0 }, tsg: GENE_TYPE.TUMOR_SUPPRESSOR },
       },
+      'type/tsg',
       {
         hugoSymbol: 'name',
         tsg: true,
@@ -52,6 +85,7 @@ describe('getGeneType', () => {
     ],
     [
       { name: 'name', type: { ocg: '', tsg: GENE_TYPE.TUMOR_SUPPRESSOR } },
+      'type/tsg',
       {
         hugoSymbol: 'name',
         tsg: true,
@@ -60,6 +94,7 @@ describe('getGeneType', () => {
     ],
     [
       { name: 'name', type: { ocg: '', tsg: '' } },
+      'type/tsg',
       {
         hugoSymbol: 'name',
         tsg: false,
@@ -68,7 +103,7 @@ describe('getGeneType', () => {
     ],
   ];
 
-  test.each(tests)('Should map to payload correctly %j', (args, expected) => {
-    expect(createGeneTypePayload(args)).toEqual(expected);
+  test.each(tests)('Should map to payload correctly %j with value path "%s"', (gene, valuePath, expected) => {
+    expect(createGeneTypePayload(gene, valuePath)).toEqual(expected);
   });
 });
diff --git a/src/main/webapp/app/shared/util/core-gene-type-submission/core-gene-type-submission.ts b/src/main/webapp/app/shared/util/core-gene-type-submission/core-gene-type-submission.ts
@@ -4,14 +4,16 @@ import { useLastReviewedOnly } from '../core-submission-shared/core-submission-u
 
 export function createGeneTypePayload(
   originalGene: Pick<Gene, 'name'> & { type: Pick<Gene['type'], 'ocg' | 'ocg_review' | 'tsg' | 'tsg_review'> },
+  valuePath: string,
 ): Required<Pick<GenePayload, 'hugoSymbol' | 'oncogene' | 'tsg'>> {
-  const gene = useLastReviewedOnly(originalGene);
+  const gene = useLastReviewedOnly(originalGene, valuePath);
   return {
     hugoSymbol: gene!.name,
     oncogene: gene!.type.ocg ? true : false,
     tsg: gene!.type.tsg ? true : false,
   };
 }
+
 export function removeGenePayload(gene: Pick<Gene, 'name'>): Required<Pick<GenePayload, 'hugoSymbol'>> {
   return {
     hugoSymbol: gene.name,

diff --git a/src/main/webapp/app/shared/util/core-submission-shared/core-submission-utils.ts b/src/main/webapp/app/shared/util/core-submission-shared/core-submission-utils.ts
@@ -1,33 +1,42 @@
 import { Review } from 'app/shared/model/firebase/firebase.model';
 
-export function useLastReviewedOnly<T>(obj: T): T | undefined {
-  function useLastReviewedOnlyRec(curObj: T): T | undefined {
+function shouldProtect(valuePath: string | undefined, path: string) {
+  return valuePath !== undefined && path.length > 0 && (path.startsWith(valuePath) || valuePath.startsWith(path));
+}
+
+export function useLastReviewedOnly<T>(obj: T, valuePath?: string): T | undefined {
+  function useLastReviewedOnlyRec(curObj: T, parentPath: string): T | undefined {
     const newObj: T = {} as T;
     for (const [key, value] of Object.entries(curObj as Record<string, unknown>)) {
+      const currentPath = `${parentPath}${parentPath.length > 0 ? '/' : ''}${key}`;
+      const protectCurrent = shouldProtect(valuePath, currentPath);
+      const protectParent = shouldProtect(valuePath, parentPath);
+
       if (key.endsWith('_review')) {
         const temp: Review = Object.assign({} as Review, value);
-        if (temp?.added) {
-          return undefined;
-        }
         (newObj as Record<string, unknown>)[key] = temp;
       } else if (Array.isArray(value)) {
         const reviewObj: Review | undefined = curObj[`${key}_review`] as Review;
-        if (reviewObj?.added) {
+        if (reviewObj?.added && !protectParent) {
           return undefined;
         }
-        const arr: T[] = [];
+        const arr: (T | undefined)[] = [];
+        let i = 0;
         for (const arrObj of value) {
-          const temp = useLastReviewedOnlyRec(arrObj);
-          if (temp !== undefined) {
+          const temp = useLastReviewedOnlyRec(arrObj, `${currentPath}/${i}`);
+          if (temp !== undefined || protectParent) {
             arr.push(temp);
           }
+          i++;
         }
         (newObj as Record<string, unknown>)[key] = arr;
       } else if (typeof value === 'object') {
-        (newObj as Record<string, unknown>)[key] = useLastReviewedOnlyRec(value as T);
+        (newObj as Record<string, unknown>)[key] = useLastReviewedOnlyRec(value as T, currentPath);
       } else {
         const reviewObj: Review | undefined = curObj[`${key}_review`] as Review;
-        if (!reviewObj?.added) {
+        if (protectCurrent) {
+          (newObj as Record<string, unknown>)[key] = value;
+        } else if (!reviewObj?.added || protectParent) {
           (newObj as Record<string, unknown>)[key] = reviewObj?.lastReviewed !== undefined ? reviewObj.lastReviewed : value;
         } else {
           return undefined;
@@ -36,5 +45,5 @@ export function useLastReviewedOnly<T>(obj: T): T | undefined {
     }
     return newObj;
   }
-  return useLastReviewedOnlyRec(obj);
+  return useLastReviewedOnlyRec(obj, '');
 }