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Fixed approve all
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@jfkonecn
jfkonecn committed Sep 23, 2024
1 parent f6a83c8 commit 522a927
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Showing 3 changed files with 171 additions and 87 deletions.
12 changes: 9 additions & 3 deletions src/main/webapp/app/service/firebase/firebase-gene-review-service.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@ import {
import { EvidenceApi } from 'app/shared/api/manual/evidence-api';
import { createGeneTypePayload, isGeneTypeChange } from 'app/shared/util/core-gene-type-submission/core-gene-type-submission';
import { GeneTypeApi } from 'app/shared/api/manual/gene-type-api';
import { flattenReviewPaths, useLastReviewedOnly } from 'app/shared/util/core-submission-shared/core-submission-utils';

export class FirebaseGeneReviewService {
firebaseRepository: FirebaseRepository;
Expand Down Expand Up @@ -130,8 +131,13 @@ export class FirebaseGeneReviewService {
let geneTypePayload: ReturnType<typeof createGeneTypePayload> | undefined = undefined;
let hasEvidences = false;
try {
for (const reviewLevel of reviewLevels) {
if (!(isCreateReview(reviewLevel) && isAcceptAll)) {
const flattenedReviewLevels = reviewLevels.flatMap(flattenReviewPaths);
// Generate a new version of the gene object (`approvedGene`) for the getEvidence payload.
// This ensures that if multiple valuePaths modify the same part of the payload,
// the changes are applied consistently, preventing any section from being overwritten unintentionally.
const approvedGene = useLastReviewedOnly(gene, ...flattenedReviewLevels.map(x => x.valuePath)) as Gene;
for (const reviewLevel of flattenedReviewLevels) {
if (!isCreateReview(reviewLevel)) {
if (reviewLevel.reviewInfo.review.removed) {
const deleteEvidencesPayload = pathToDeleteEvidenceArgs({ valuePath: reviewLevel.valuePath, gene });
if (deleteEvidencesPayload !== undefined) {
Expand All @@ -141,7 +147,7 @@ export class FirebaseGeneReviewService {
geneTypePayload = createGeneTypePayload(gene, reviewLevel.valuePath);
} else {
const args = pathToGetEvidenceArgs({
gene,
gene: approvedGene,
valuePath: reviewLevel.valuePath,
updateTime: new Date().getTime(),
drugListRef,
Expand Down
169 changes: 133 additions & 36 deletions src/main/webapp/app/shared/util/core-submission-shared/core-submission-utils.spec.ts
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Original file line number Diff line number Diff line change
@@ -1,8 +1,9 @@
import 'jest-expect-message';
import { findAllChildReviewPaths, useLastReviewedOnly } from './core-submission-utils';
import { flattenReviewPaths, useLastReviewedOnly } from './core-submission-utils';
import { Gene } from 'app/shared/model/firebase/firebase.model';
import { GENE_TYPE } from 'app/config/constants/firebase';
import _ from 'lodash';
import { BaseReviewLevel, ReviewLevel } from '../firebase/firebase-review-utils';

type RecursivePartial<T> = {
[P in keyof T]?: RecursivePartial<T[P]>;
Expand Down Expand Up @@ -206,47 +207,143 @@ describe('useLastReviewedOnly', () => {
});

describe('findAllChildReviewPaths', () => {
const tests: [RecursivePartial<Gene>, string, string[]][] = [
const tests: [
RecursivePartial<ReviewLevel & { children?: (ReviewLevel & { children?: ReviewLevel[] })[] }>[],
RecursivePartial<ReviewLevel>[],
][] = [
[
{
summary: 'XXXXXXXXXXX',
summary_review: {
lastReviewed: 'YYYYYYYYYYY',
added: true,
updateTime: 0,
updatedBy: 'Test User',
},
},
'summary',
['summary'],
],
[
{
summary: 'XXXXXXXXXXX',
summary_review: {
lastReviewed: 'YYYYYYYYYYY',
updateTime: 0,
updatedBy: 'Test User',
[
{
valuePath: 'mutations/12/name',
children: [
{
valuePath: 'mutations/12/name/mutation_effect',
children: [
{
valuePath: 'mutations/12/mutation_effect/description',
children: [],
reviewInfo: {
reviewPath: 'mutations/12/mutation_effect/description_review',
reviewAction: 2,
},
},
{
valuePath: 'mutations/12/mutation_effect/effect',
children: [],
reviewInfo: {
reviewPath: 'mutations/12/mutation_effect/effect_review',
reviewAction: 2,
},
},
{
valuePath: 'mutations/12/mutation_effect/oncogenic',
children: [],
reviewInfo: {
reviewPath: 'mutations/12/mutation_effect/oncogenic_review',
reviewAction: 2,
},
},
],
},
],
reviewInfo: {
reviewPath: 'mutations/12/name_review',
reviewAction: 0,
},
},
mutations: [
{
name: '',
name_review: {
lastReviewed: 'YYYYYYYYYYY',
updateTime: 0,
updatedBy: 'Test User',
{
valuePath: 'mutations/13/name',
children: [
{
children: [
{
valuePath: 'mutations/13/mutation_effect/description',
children: [],
reviewInfo: {
reviewPath: 'mutations/13/mutation_effect/description_review',
reviewAction: 2,
},
},
{
valuePath: 'mutations/13/mutation_effect/effect',
children: [],
reviewInfo: {
reviewPath: 'mutations/13/mutation_effect/effect_review',
reviewAction: 2,
},
},
{
valuePath: 'mutations/13/mutation_effect/oncogenic',
children: [],
reviewInfo: {
reviewPath: 'mutations/13/mutation_effect/oncogenic_review',
reviewAction: 2,
},
},
],
},
],
reviewInfo: {
reviewPath: 'mutations/13/name_review',
reviewAction: 0,
},
],
},
'mutations/0',
['mutations/0/name'],
},
],
[
{
valuePath: 'mutations/12/mutation_effect/description',
children: [],
reviewInfo: {
reviewPath: 'mutations/12/mutation_effect/description_review',
reviewAction: 2,
},
},
{
valuePath: 'mutations/12/mutation_effect/effect',
children: [],
reviewInfo: {
reviewPath: 'mutations/12/mutation_effect/effect_review',
reviewAction: 2,
},
},
{
valuePath: 'mutations/12/mutation_effect/oncogenic',
children: [],
reviewInfo: {
reviewPath: 'mutations/12/mutation_effect/oncogenic_review',
reviewAction: 2,
},
},
{
valuePath: 'mutations/13/mutation_effect/description',
children: [],
reviewInfo: {
reviewPath: 'mutations/13/mutation_effect/description_review',
reviewAction: 2,
},
},
{
valuePath: 'mutations/13/mutation_effect/effect',
children: [],
reviewInfo: {
reviewPath: 'mutations/13/mutation_effect/effect_review',
reviewAction: 2,
},
},
{
valuePath: 'mutations/13/mutation_effect/oncogenic',
children: [],
reviewInfo: {
reviewPath: 'mutations/13/mutation_effect/oncogenic_review',
reviewAction: 2,
},
},
],
],
];

test.each(tests)('Should find all child review paths in %j for path "%s"', (gene, path, expected) => {
const geneCopy = _.cloneDeep(gene);
expect(findAllChildReviewPaths(gene as Gene, path)).toEqual(expected);
expect(geneCopy, 'The passed gene should be untouched').toEqual(gene);
test.each(tests)('Should find all child review paths in %j for path "%s"', (reviews, expected) => {
const actual = reviews.flatMap(x => flattenReviewPaths(x as BaseReviewLevel));
expect(actual).toEqual(expected);
});
});
77 changes: 29 additions & 48 deletions src/main/webapp/app/shared/util/core-submission-shared/core-submission-utils.ts
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Original file line number Diff line number Diff line change
@@ -1,17 +1,24 @@
import { Gene, Review } from 'app/shared/model/firebase/firebase.model';
import { Review } from 'app/shared/model/firebase/firebase.model';
import { BaseReviewLevel, ReviewLevel } from '../firebase/firebase-review-utils';

/**
* Determines whether the `path` should be protected based on the review path.
*
* Protection is based on whether the current path or parent path aligns with the `reviewPath`,
* meaning that the data was just accepted by a user.
*
* @param reviewPath - The reference path for review, indicating an accepted field. Undefined when nothing was accepted.
* @param [reviewPaths] - The reference path for review, indicating an accepted field. Undefined when nothing was accepted.
* @param path - The path of the current element being evaluated.
* @returns - Returns true if the `path` should be protected, false otherwise.
*/
function isPathProtected(reviewPath: string | undefined, path: string): boolean {
return reviewPath !== undefined && path.length > 0 && (path.includes(reviewPath) || reviewPath.includes(path));
function isPathProtected(reviewPaths: string[], path: string): boolean {
for (const reviewPath of reviewPaths) {
const shouldProtect = reviewPath !== undefined && path.length > 0 && (path.includes(reviewPath) || reviewPath.includes(path));
if (shouldProtect) {
return true;
}
}
return false;
}

/**
Expand All @@ -23,17 +30,17 @@ function isPathProtected(reviewPath: string | undefined, path: string): boolean
* only use their`lastReviewed` value.
*
* @param obj - The object to be filtered for last reviewed elements.
* @param [reviewPath] - The path used to determine if an element should be protected.
* @param [reviewPaths] - The paths used to determine if an element should be protected.
* @returns - The filtered object or undefined if no elements are accepted.
*/
export function useLastReviewedOnly<T>(obj: T, reviewPath?: string): T | undefined {
export function useLastReviewedOnly<T>(obj: T, ...reviewPaths: string[]): T | undefined {
function processObjectRecursively(currentObj: T, parentPath: string): T | undefined {
const resultObj: T = {} as T;

for (const [key, value] of Object.entries(currentObj as Record<string, unknown>)) {
const currentPath = `${parentPath}${parentPath.length > 0 ? '/' : ''}${key}`;
const isCurrentPathProtected = isPathProtected(reviewPath, currentPath);
const isParentPathProtected = isPathProtected(reviewPath, parentPath);
const isCurrentPathProtected = isPathProtected(reviewPaths, currentPath);
const isParentPathProtected = isPathProtected(reviewPaths, parentPath);

// If the key ends with "_review", copy it to the new object
if (key.endsWith('_review')) {
Expand Down Expand Up @@ -84,48 +91,22 @@ export function useLastReviewedOnly<T>(obj: T, reviewPath?: string): T | undefin
return processObjectRecursively(obj, '');
}

export function findAllChildReviewPaths(gene: Gene, reviewPath: string): string[] {
const objectKeys = reviewPath.split('/');
let pathObject: unknown = gene;
export function flattenReviewPaths(reviewLevel: BaseReviewLevel): ReviewLevel[] {
const arr: ReviewLevel[] = [];

{
let currentPath = '';
for (const objectKey of objectKeys) {
currentPath += `/${objectKey}`;
if (Array.isArray(pathObject) || (typeof pathObject === 'object' && pathObject !== null)) {
pathObject = pathObject[objectKey];
} else {
throw new Error(`${currentPath} is not an object or array in the path "${reviewPath}" "${JSON.stringify(pathObject)}"`);
}
if (reviewLevel.children !== undefined && reviewLevel.children.length > 0) {
for (const childLevel of reviewLevel.children) {
arr.push(...flattenReviewPaths(childLevel));
}
} else if (
'reviewInfo' in reviewLevel &&
typeof reviewLevel.reviewInfo === 'object' &&
reviewLevel.reviewInfo !== null &&
'reviewAction' in reviewLevel.reviewInfo &&
reviewLevel.reviewInfo.reviewAction !== undefined
) {
arr.push(reviewLevel as ReviewLevel);
}

if (typeof pathObject !== 'object' || pathObject === null) {
return [reviewPath];
}

function findAllChildReviewPathsRecursively(obj: unknown, currentPath: string): string[] {
if (currentPath.endsWith('_review')) {
return [currentPath.replace('_review', '')];
} else if (Array.isArray(obj)) {
const arr: string[] = [];
let i = 0;
for (const element of obj) {
const temp = findAllChildReviewPathsRecursively(element, `${currentPath}/${i}`);
arr.push(...temp);
i++;
}
return arr;
} else if (typeof obj === 'object' && obj !== null) {
const arr: string[] = [];
for (const [key, value] of Object.entries(obj)) {
const temp = findAllChildReviewPathsRecursively(value, `${currentPath}/${key}`);
arr.push(...temp);
}
return arr;
} else {
return [];
}
}
return findAllChildReviewPathsRecursively(pathObject, reviewPath);
return arr;
}

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