diff --git a/.env.example b/.env.example index 74ab654..6c7b861 100644 --- a/.env.example +++ b/.env.example @@ -16,14 +16,8 @@ MAX_NUMBER_OF_GF_SUGGESTIONS= GENES_SUGGESTIONS_INDEX_NAME= VARIANTS_SUGGESTIONS_INDEX_NAME= -# SQS configuration -SEND_UPDATE_TO_SQS= -SQS_QUEUE_URL= MAX_SET_CONTENT_SIZE= -# Riff -RIFF_URL= - # Index names ES_FILE_INDEX= ES_STUDY_INDEX= diff --git a/package-lock.json b/package-lock.json index 2f9302f..27fdce1 100644 --- a/package-lock.json +++ b/package-lock.json @@ -13,7 +13,6 @@ "@arranger/middleware": "^2.16.0", "@arranger/server": "^2.16.1", "@awaitjs/express": "^0.8.0", - "@aws-sdk/client-sqs": "^3.438.0", "@elastic/elasticsearch": "^7.9.1", "ajv": "^8.12.0", "cors": "2.8.5", @@ -288,688 +287,6 @@ "express": "4.x" } }, - "node_modules/@aws-crypto/crc32": { - "version": "3.0.0", - "resolved": "https://registry.npmjs.org/@aws-crypto/crc32/-/crc32-3.0.0.tgz", - "integrity": "sha512-IzSgsrxUcsrejQbPVilIKy16kAT52EwB6zSaI+M3xxIhKh5+aldEyvI+z6erM7TCLB2BJsFrtHjp6/4/sr+3dA==", - 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} - }, "fastq": { "version": "1.13.0", "resolved": "https://registry.npmjs.org/fastq/-/fastq-1.13.0.tgz", @@ -21698,11 +18917,6 @@ "integrity": "sha512-BrpvfNAE3dcvq7ll3xVumzjKjZQ5tI1sEUIKr3Uoks0XUl45St3FlatVqef9prk4jRDzhW6WZg+3bk93y6pLjA==", "dev": true }, - "strnum": { - "version": "1.0.5", - "resolved": "https://registry.npmjs.org/strnum/-/strnum-1.0.5.tgz", - "integrity": "sha512-J8bbNyKKXl5qYcR36TIO8W3mVGVHrmmxsd5PAItGkmyzwJvybiw2IVq5nqd0i4LSNSkB/sx9VHllbfFdr9k1JA==" - }, "subscriptions-transport-ws": { "version": "0.9.19", "resolved": "https://registry.npmjs.org/subscriptions-transport-ws/-/subscriptions-transport-ws-0.9.19.tgz", diff --git a/package.json b/package.json index 59c2405..8f51d8f 100644 --- a/package.json +++ b/package.json @@ -39,7 +39,6 @@ "@arranger/middleware": "^2.16.0", "@arranger/server": "^2.16.1", "@awaitjs/express": "^0.8.0", - "@aws-sdk/client-sqs": "^3.438.0", "@elastic/elasticsearch": "^7.9.1", "ajv": "^8.12.0", "cors": "2.8.5", diff --git a/src/ElasticSearchClientInstance.ts b/src/ElasticSearchClientInstance.ts index b8f51bb..1521527 100644 --- a/src/ElasticSearchClientInstance.ts +++ b/src/ElasticSearchClientInstance.ts @@ -8,10 +8,8 @@ class EsInstance { constructor() { if (!this.instance) { if (esUser && esPass) { - console.debug('Using basic auth'); this.instance = new Client({ node: esHost, auth: { username: esUser, password: esPass } }); } else { - console.debug('Not using basic auth'); this.instance = new Client({ node: esHost }); } } diff --git a/src/SQS/eventTypes.ts b/src/SQS/eventTypes.ts deleted file mode 100644 index 52f0243..0000000 --- a/src/SQS/eventTypes.ts +++ /dev/null @@ -1,48 +0,0 @@ -import { SetSqon } from '../endpoints/sets/setsTypes'; - -export type EventCreate = { - actionType: string; - values: EventCreateValue; -}; - -export type EventCreateValue = { - setId: string; - createdAt: Date; - ids: string[]; - size: number; - sqon: SetSqon; - type: string; - userId: string; - path: string; - tag: string; -}; - -export type EventDelete = { - actionType: string; - values: EventDeleteValues; -}; - -export type EventDeleteValues = { - userId: string; - setIds: string[]; -}; - -export type EventUpdate = { - actionType: string; - subActionType: string; - values: UpdateTagValue | UpdateContentValue; -}; - -export type UpdateTagValue = { - userId: string; - setId: string; - newTag: string; -}; - -export type UpdateContentValue = { - userId: string; - ids: string[]; - setId: string; - createdAt: Date; - tag: string; -}; diff --git a/src/SQS/sendEvent.ts b/src/SQS/sendEvent.ts deleted file mode 100644 index 2f7b7a3..0000000 --- a/src/SQS/sendEvent.ts +++ /dev/null @@ -1,18 +0,0 @@ -import { SendMessageCommand, SendMessageCommandOutput, SQSClient } from '@aws-sdk/client-sqs'; - -import { sqsQueueUrl } from '../env'; -import { EventCreate, EventDelete, EventUpdate } from './eventTypes'; - -export const sendSetInSQSQueue = async ( - sqs: SQSClient, - data: EventCreate | EventUpdate | EventDelete, -): Promise => { - const command = new SendMessageCommand({ - QueueUrl: sqsQueueUrl, - DelaySeconds: 10, - MessageAttributes: {}, - MessageBody: JSON.stringify(data), - }); - const response = await sqs.send(command); - return response; -}; diff --git a/src/app.test.ts b/src/app.test.ts index 0c615b1..c3b7e19 100644 --- a/src/app.test.ts +++ b/src/app.test.ts @@ -1,4 +1,3 @@ -import { SQSClient } from '@aws-sdk/client-sqs'; import { Express } from 'express'; import Keycloak from 'keycloak-connect'; import request from 'supertest'; @@ -6,7 +5,6 @@ import request from 'supertest'; import { fakeKeycloakClient, fakeKeycloakRealm, fakeKeycloakUrl, getToken, publicKey } from '../test/authTestUtils'; import buildApp from './app'; import { ArrangerProject } from './arrangerUtils'; -import { searchAllSources } from './endpoints/searchByIds/searchAllSources'; import { SetNotFoundError } from './endpoints/sets/setError'; import { createSet, @@ -18,11 +16,9 @@ import { } from './endpoints/sets/setsFeature'; import { Set, UpdateSetContentBody, UpdateSetTagBody } from './endpoints/sets/setsTypes'; import { getStatistics, getStudiesStatistics, Statistics } from './endpoints/statistics'; -import { RiffError } from './riff/riffError'; jest.mock('./endpoints/sets/setsFeature'); jest.mock('./endpoints/statistics'); -jest.mock('./endpoints/searchByIds/searchAllSources'); describe('Express app (without Arranger)', () => { let app: Express; @@ -31,7 +27,6 @@ describe('Express app (without Arranger)', () => { const getProject = (_s: string) => ({} as ArrangerProject); beforeEach(() => { - const sqs = new SQSClient({}); const publicKeyToVerify = publicKey; keycloakFakeConfig = { realm: fakeKeycloakRealm, @@ -43,7 +38,7 @@ describe('Express app (without Arranger)', () => { 'realm-public-key': publicKeyToVerify, // For test purpose, we use public key to validate token. }; const keycloak = new Keycloak({}, keycloakFakeConfig); - app = buildApp(keycloak, sqs, getProject); // Re-create app between each test to ensure isolation between tests. + app = buildApp(keycloak, getProject); // Re-create app between each test to ensure isolation between tests. }); it('GET /status (public) should responds with json', async () => { @@ -274,21 +269,6 @@ describe('Express app (without Arranger)', () => { .expect(200, expectedSets); expect((getSets as jest.Mock).mock.calls.length).toEqual(1); }); - - it('should return 500 if Authorization header contains valid token but an error occurs', async () => { - const expectedError = new RiffError(404, { message: 'OOPS' }); - (getSets as jest.Mock).mockImplementation(() => { - throw expectedError; - }); - - const token = getToken(); - - await request(app) - .get('/sets') - .set({ Authorization: `Bearer ${token}` }) - .expect(500, { error: 'Internal Server Error' }); - expect((getSets as jest.Mock).mock.calls.length).toEqual(1); - }); }); describe('POST /sets', () => { @@ -344,23 +324,6 @@ describe('Express app (without Arranger)', () => { .expect(200); expect((createSet as jest.Mock).mock.calls.length).toEqual(1); }); - - it('should return 500 if Authorization header contains valid token but an error occurs', async () => { - const expectedError = new RiffError(400, { message: 'OOPS' }); - (createSet as jest.Mock).mockImplementation(() => { - throw expectedError; - }); - - const token = getToken(); - - await request(app) - .post('/sets') - .send(requestBody) - .set('Content-type', 'application/json') - .set({ Authorization: `Bearer ${token}` }) - .expect(500, { error: 'Internal Server Error' }); - expect((createSet as jest.Mock).mock.calls.length).toEqual(1); - }); }); describe('PUT /sets/:setId', () => { @@ -420,11 +383,11 @@ describe('Express app (without Arranger)', () => { .set({ Authorization: `Bearer ${token}` }) .expect(checkRes) .expect(200); + expect((updateSetTag as jest.Mock).mock.calls.length).toEqual(1); expect((updateSetTag as jest.Mock).mock.calls[0][0]).toEqual(updateSetTagBody); expect((updateSetTag as jest.Mock).mock.calls[0][1]).toEqual(`Bearer ${token}`); - expect((updateSetTag as jest.Mock).mock.calls[0][2]).toEqual(userId); - expect((updateSetTag as jest.Mock).mock.calls[0][3]).toEqual('1eh'); + expect((updateSetTag as jest.Mock).mock.calls[0][2]).toEqual('1eh'); }); it('should return 200 if Authorization header contains valid token and no error occurs - update content', async () => { @@ -496,71 +459,5 @@ describe('Express app (without Arranger)', () => { .expect(200, 'true'); expect((deleteSet as jest.Mock).mock.calls.length).toEqual(1); }); - - it('should return 500 if Authorization header contains valid token but an error occurs', async () => { - const expectedError = new RiffError(404, { message: 'OOPS' }); - (deleteSet as jest.Mock).mockImplementation(() => { - throw expectedError; - }); - - const token = getToken(); - - await request(app) - .delete('/sets/1ei') - .set('Content-type', 'application/json') - .set({ Authorization: `Bearer ${token}` }) - .expect(500, { error: 'Internal Server Error' }); - expect((deleteSet as jest.Mock).mock.calls.length).toEqual(1); - }); - }); - - describe('POST /searchByIds', () => { - const requestBody = { - project: '2021_05_03_v2', - ids: ['PT_HXDR3ZX6'], - }; - - beforeEach(() => { - (searchAllSources as jest.Mock).mockReset(); - }); - - it('should return 403 if no Authorization header', () => - request(app) - .post('/searchByIds') - .expect(403)); - - it('should return 200 if Authorization header contains valid token and no error occurs', async () => { - const mockSearchByIdsResponse = [ - { search: 'PT_HXDR3ZX6', type: 'PARTICIPANT', participantIds: ['PT_HXDR3ZX6'] }, - ]; - (searchAllSources as jest.Mock).mockImplementation(() => mockSearchByIdsResponse); - - const token = getToken(); - - await request(app) - .post('/searchByIds') - .send(requestBody) - .set('Content-type', 'application/json') - .set({ Authorization: `Bearer ${token}` }) - .expect(200, { participants: mockSearchByIdsResponse }); - expect((searchAllSources as jest.Mock).mock.calls.length).toEqual(1); - }); - - it('should return 500 if Authorization header contains valid token but an error occurs', async () => { - const expectedError = new Error('OOPS'); - (searchAllSources as jest.Mock).mockImplementation(() => { - throw expectedError; - }); - - const token = getToken(); - - await request(app) - .post('/searchByIds') - .send(requestBody) - .set('Content-type', 'application/json') - .set({ Authorization: `Bearer ${token}` }) - .expect(500, { error: 'Internal Server Error' }); - expect((searchAllSources as jest.Mock).mock.calls.length).toEqual(1); - }); }); }); diff --git a/src/app.ts b/src/app.ts index 503124c..0564574 100644 --- a/src/app.ts +++ b/src/app.ts @@ -1,5 +1,4 @@ import addAsync from '@awaitjs/express'; -import { SQSClient } from '@aws-sdk/client-sqs'; import cors from 'cors'; import express, { Express } from 'express'; import { Keycloak } from 'keycloak-connect'; @@ -10,8 +9,6 @@ import { ArrangerProject } from './arrangerUtils'; import { computeAuthorizedStudiesForAllFences } from './endpoints/authorizedStudies/computeAuthorizedStudies'; import genomicFeatureSuggestions, { SUGGESTIONS_TYPES } from './endpoints/genomicFeatureSuggestions'; import { getPhenotypesNodes } from './endpoints/phenotypes'; -import { searchAllSources } from './endpoints/searchByIds/searchAllSources'; -import { SearchByIdsResult } from './endpoints/searchByIds/searchByIdsTypes'; import { createSet, deleteSet, @@ -28,7 +25,7 @@ import { STATISTICS_CACHE_ID, STATISTICS_PUBLIC_CACHE_ID, verifyCache } from './ import { injectBodyHttpHeaders } from './middleware/injectBodyHttpHeaders'; import { resolveSetIdMiddleware } from './middleware/resolveSetIdInSqon'; -export default (keycloak: Keycloak, sqs: SQSClient, getProject: (projectId: string) => ArrangerProject): Express => { +export default (keycloak: Keycloak, getProject: (projectId: string) => ArrangerProject): Express => { const app = addAsync.addAsync(express()); const cache = new NodeCache({ stdTTL: cacheTTL }); @@ -88,18 +85,9 @@ export default (keycloak: Keycloak, sqs: SQSClient, getProject: (projectId: stri res.json(data); }); - app.postAsync('/searchByIds', keycloak.protect(), async (req, res) => { - const ids: string[] = req.body.ids; - const projectId: string = req.body.project; - const participants: SearchByIdsResult[] = await searchAllSources(ids, projectId, getProject); - - res.send({ participants }); - }); - app.getAsync('/sets', keycloak.protect(), async (req, res) => { const accessToken = req.headers.authorization; - const userId = req['kauth']?.grant?.access_token?.content?.sub; - const userSets = await getSets(accessToken, userId); + const userSets = await getSets(accessToken); res.send(userSets); }); @@ -107,7 +95,7 @@ export default (keycloak: Keycloak, sqs: SQSClient, getProject: (projectId: stri app.postAsync('/sets', keycloak.protect(), async (req, res) => { const accessToken = req.headers.authorization; const userId = req['kauth']?.grant?.access_token?.content?.sub; - const createdSet = await createSet(req.body as CreateSetBody, accessToken, userId, sqs, getProject); + const createdSet = await createSet(req.body as CreateSetBody, accessToken, userId, getProject); res.send(createdSet); }); @@ -120,14 +108,13 @@ export default (keycloak: Keycloak, sqs: SQSClient, getProject: (projectId: stri let updatedSet: Set; if (requestBody.subAction === SubActionTypes.RENAME_TAG) { - updatedSet = await updateSetTag(requestBody as UpdateSetTagBody, accessToken, userId, setId, sqs); + updatedSet = await updateSetTag(requestBody as UpdateSetTagBody, accessToken, setId); } else { updatedSet = await updateSetContent( requestBody as UpdateSetContentBody, accessToken, userId, setId, - sqs, getProject, ); } @@ -136,17 +123,15 @@ export default (keycloak: Keycloak, sqs: SQSClient, getProject: (projectId: stri app.deleteAsync('/sets/:setId', keycloak.protect(), async (req, res) => { const accessToken = req.headers.authorization; - const userId = req['kauth']?.grant?.access_token?.content?.sub; const setId: string = req.params.setId; - const deletedResult = await deleteSet(accessToken, setId, userId, sqs); + const deletedResult = await deleteSet(accessToken, setId); res.send(deletedResult); }); app.postAsync('/phenotypes', keycloak.protect(), async (req, res) => { const accessToken = req.headers.authorization; - const userId = req['kauth']?.grant?.access_token?.content?.sub; const sqon: SetSqon = req.body.sqon; const type: string = req.body.type; const projectId: string = req.body.project; @@ -158,7 +143,6 @@ export default (keycloak: Keycloak, sqs: SQSClient, getProject: (projectId: stri type, aggregations_filter_themselves, accessToken, - userId, ); res.send({ data }); diff --git a/src/endpoints/phenotypes.ts b/src/endpoints/phenotypes.ts index 809cb63..2daff7c 100644 --- a/src/endpoints/phenotypes.ts +++ b/src/endpoints/phenotypes.ts @@ -105,9 +105,8 @@ export const getPhenotypesNodes = async ( type: string, aggregations_filter_themselves: boolean, accessToken: string, - userId: string, ) => { - const newSqon = await replaceSetByIds(sqon, accessToken, userId); + const newSqon = await replaceSetByIds(sqon, accessToken); const participantIds = await getParticipantIds(newSqon as SetSqon, projectId, getProject); diff --git a/src/endpoints/searchByIds/byBiospecimenId.ts b/src/endpoints/searchByIds/byBiospecimenId.ts deleted file mode 100644 index 637c387..0000000 --- a/src/endpoints/searchByIds/byBiospecimenId.ts +++ /dev/null @@ -1,65 +0,0 @@ -import { CONSTANTS } from '@arranger/middleware'; -import { get } from 'lodash'; - -import { idKey } from '../../env'; -import { SetSqon } from '../sets/setsTypes'; -import { SearchByIdsResult, SourceType } from './searchByIdsTypes'; - -const query = `query ($sqon: JSON, $size: Int, $offset: Int) { - participant { - hits (filters: $sqon, first:$size, offset:$offset){ - edges { - node { - ${idKey} - biospecimens { - hits { - edges { - node { - ${idKey} - } - } - } - } - } - } - } - } -}`; - -const getSqon = (ids = []): SetSqon => ({ - op: CONSTANTS.AND_OP, - content: [ - { - op: CONSTANTS.IN_OP, - content: { - field: `biospecimens.${idKey}`, - value: ids, - }, - }, - ], -}); - -const transform = (data: unknown, ids: string[]): SearchByIdsResult[] => { - const participants = get(data, 'participant', []).filter(p => !!p); - - return ids.map(id => { - const participantIds = participants - .filter(participant => { - const biospecimens = get(participant, 'biospecimens', []); - return biospecimens.some(bio => bio[idKey] === id); - }) - .map(participant => participant[idKey]); - - return { - search: id, - type: 'BIOSPECIMEN', - participantIds, - }; - }); -}; - -export const byBiospecimenId: SourceType = { - query, - getSqon, - transform, -}; diff --git a/src/endpoints/searchByIds/byFamilyId.ts b/src/endpoints/searchByIds/byFamilyId.ts deleted file mode 100644 index 242c9d7..0000000 --- a/src/endpoints/searchByIds/byFamilyId.ts +++ /dev/null @@ -1,54 +0,0 @@ -import { CONSTANTS } from '@arranger/middleware'; -import { get } from 'lodash'; - -import { idKey } from '../../env'; -import { SetSqon } from '../sets/setsTypes'; -import { SearchByIdsResult, SourceType } from './searchByIdsTypes'; - -const query = `query ($sqon: JSON, $size: Int, $offset: Int) { - participant { - hits (filters: $sqon, first:$size, offset:$offset){ - edges { - node { - ${idKey} - family_id - } - } - } - } -}`; - -const getSqon = (ids = []): SetSqon => ({ - op: CONSTANTS.OR_OP, - content: [ - { - op: CONSTANTS.IN_OP, - content: { - field: 'family_id', - value: ids, - }, - }, - ], -}); - -const transform = (data: unknown, ids: string[]): SearchByIdsResult[] => { - const participants = get(data, 'participant', []).filter(p => !!p); - - return ids.map(id => { - const participantIds = participants - .filter(participant => participant.family_id === id) - .map(participant => participant[idKey]); - - return { - search: id, - type: 'FAMILY', - participantIds, - }; - }); -}; - -export const byFamilyId: SourceType = { - query, - getSqon, - transform, -}; diff --git a/src/endpoints/searchByIds/byId.ts b/src/endpoints/searchByIds/byId.ts deleted file mode 100644 index 680c884..0000000 --- a/src/endpoints/searchByIds/byId.ts +++ /dev/null @@ -1,61 +0,0 @@ -import { CONSTANTS } from '@arranger/middleware'; -import { get } from 'lodash'; - -import { idKey } from '../../env'; -import { SetSqon } from '../sets/setsTypes'; -import { SearchByIdsResult, SourceType } from './searchByIdsTypes'; - -const query = `query ($sqon: JSON, $size: Int, $offset: Int) { - participant { - hits (filters: $sqon, first:$size, offset:$offset){ - edges { - node { - ${idKey} - external_id - } - } - } - } -}`; - -const getSqon = (ids = []): SetSqon => ({ - op: CONSTANTS.OR_OP, - content: [ - { - op: CONSTANTS.IN_OP, - content: { - field: `${idKey}`, - value: ids, - }, - }, - { - op: CONSTANTS.IN_OP, - content: { - field: 'external_id', - value: ids, - }, - }, - ], -}); - -const transform = (data: unknown, ids: string[]): SearchByIdsResult[] => { - const participants = get(data, 'participant', []).filter(p => !!p); - - return ids.map(id => { - const participantIds = participants - .filter(participant => participant[idKey] === id || participant.external_id === id) - .map(participant => participant[idKey]); - - return { - search: id, - type: 'PARTICIPANT', - participantIds, - }; - }); -}; - -export const byId: SourceType = { - query, - getSqon, - transform, -}; diff --git a/src/endpoints/searchByIds/bySampleExternalId.ts b/src/endpoints/searchByIds/bySampleExternalId.ts deleted file mode 100644 index 819e995..0000000 --- a/src/endpoints/searchByIds/bySampleExternalId.ts +++ /dev/null @@ -1,65 +0,0 @@ -import { CONSTANTS } from '@arranger/middleware'; -import { get } from 'lodash'; - -import { idKey } from '../../env'; -import { SetSqon } from '../sets/setsTypes'; -import { SearchByIdsResult, SourceType } from './searchByIdsTypes'; - -const query = `query ($sqon: JSON, $size: Int, $offset: Int) { - participant { - hits (filters: $sqon, first:$size, offset:$offset){ - edges { - node { - ${idKey} - biospecimens { - hits { - edges { - node { - external_sample_id - } - } - } - } - } - } - } - } -}`; - -const getSqon = (ids = []): SetSqon => ({ - op: CONSTANTS.AND_OP, - content: [ - { - op: CONSTANTS.IN_OP, - content: { - field: 'biospecimens.external_sample_id', - value: ids, - }, - }, - ], -}); - -const transform = (data: unknown, ids: string[]): SearchByIdsResult[] => { - const participants = get(data, 'participant', []).filter(p => !!p); - - return ids.map(id => { - const participantIds = participants - .filter(participant => { - const biospecimens = get(participant, 'biospecimens', []); - return biospecimens.some(bio => bio.external_sample_id === id); - }) - .map(participant => participant[idKey]); - - return { - search: id, - type: 'SAMPLE EXTERNAL ID', - participantIds, - }; - }); -}; - -export const bySampleExternalId: SourceType = { - query, - getSqon, - transform, -}; diff --git a/src/endpoints/searchByIds/executePagedQuery.ts b/src/endpoints/searchByIds/executePagedQuery.ts deleted file mode 100644 index 37964be..0000000 --- a/src/endpoints/searchByIds/executePagedQuery.ts +++ /dev/null @@ -1,39 +0,0 @@ -import { get } from 'lodash'; - -import { ArrangerProject } from '../../arrangerUtils'; -import { SetSqon } from '../sets/setsTypes'; -import { normalizeResults } from './normalizeResults'; - -const pageSize = 1000; - -const runPagedQuery = async (project: ArrangerProject, query: string, sqon: SetSqon) => { - let complete = false; - let offset = 0; - const results = {}; - - while (!complete) { - const queryResults = await project.runQuery({ - query, - variables: { sqon, size: pageSize, offset }, - }); - - const normalizedResults = normalizeResults(get(queryResults, 'data', {})); - - // NOTE: does not support multiple entities in a query, yet. - const entityType = Object.keys(normalizedResults)[0]; - const edges = get(normalizedResults, entityType, []); - offset += pageSize; - if (edges.length < pageSize) { - complete = true; - } - - if (!Array.isArray(results[entityType])) { - results[entityType] = []; - } - results[entityType] = results[entityType].concat(normalizedResults[entityType]); - } - - return results; -}; - -export default runPagedQuery; diff --git a/src/endpoints/searchByIds/normalizeResults.test.ts b/src/endpoints/searchByIds/normalizeResults.test.ts deleted file mode 100644 index 145e985..0000000 --- a/src/endpoints/searchByIds/normalizeResults.test.ts +++ /dev/null @@ -1,72 +0,0 @@ -import { normalizeResults } from './normalizeResults'; - -const getMockResults = () => ({ - data: { - participant: { - hits: { - edges: [ - { - node: { - kf_id: 'PT_CYBYN18G', - biospecimens: { - hits: { - edges: [ - { - node: { - kf_id: 'BS_T1SNKF50', - }, - }, - { - node: { - kf_id: 'BS_C5SDFG56', - }, - }, - ], - }, - }, - }, - }, - { - node: { - kf_id: 'PT_DJFU48GR', - biospecimens: { - hits: { - edges: [], - }, - }, - }, - }, - ], - }, - }, - }, -}); - -describe('normalizeResults', () => { - let normalized; - - beforeEach(() => { - const mockResult = getMockResults(); - normalized = normalizeResults(mockResult.data); - }); - - it('shortcuts "hits.edges" properties', () => { - expect(normalized.participant).toBeInstanceOf(Array); - expect(normalized.participant.length).toEqual(2); - }); - - it('shortcuts "hits.edges" properties recursively', () => { - expect(normalized.participant[0].biospecimens).toBeInstanceOf(Array); - expect(normalized.participant.length).toEqual(2); - }); - - it('shortcuts "node" property', () => { - expect(normalized.participant[0]).not.toHaveProperty('node'); - expect(normalized.participant[0]).toHaveProperty('kf_id'); - }); - - it('shortcuts "node" property recursively', () => { - expect(normalized.participant[0].biospecimens[0]).not.toHaveProperty('node'); - expect(normalized.participant[0]).toHaveProperty('kf_id'); - }); -}); diff --git a/src/endpoints/searchByIds/normalizeResults.ts b/src/endpoints/searchByIds/normalizeResults.ts deleted file mode 100644 index bd37c5d..0000000 --- a/src/endpoints/searchByIds/normalizeResults.ts +++ /dev/null @@ -1,69 +0,0 @@ -import { get } from 'lodash'; - -/** - * Normalizes the results of a graphql query to make it easier to manipulate, - * turning hits to plain arrays and removing extra 'node' level. - * @example - * result: - * { - * "participant": { - * "hits": { - * "edges": [{ - * "node": { - * "kf_id": "PT_CYBYN18G", - * "biospecimens": { - * "hits": { - * "edges": [{ - * "node": { - * "kf_id": "BS_T1SNKF50" - * } - * }] - * } - * } - * } - * }] - * } - * } - * } - * becomes: - * { - * "participant": [{ - * "kf_id": "PT_CYBYN18G", - * "biospecimens": [{ - * "kf_id": "BS_T1SNKF50" - * }] - * }] - * } - * @param {Object} results - The result of a graphql query - * @returns {Object} a normalized result (see example). - */ -export const normalizeResults = results => { - if (Array.isArray(results)) { - return results.map(normalizeResults); - } - - // detect 'hits: { edges: [] }' and shortcut it - const hits = get(results, 'hits.edges', null); - if (hits !== null) { - return normalizeResults(hits); - } - - if (typeof results === 'object' && results !== null) { - return Object.keys(results).reduce((norm, key) => { - const prop = results[key]; - - // detect 'node' and shortcut them - if (key === 'node' && typeof prop === 'object' && prop !== null) { - return Object.keys(prop).reduce((acc, p) => { - acc[p] = normalizeResults(prop[p]); - return acc; - }, norm); - } - - norm[key] = normalizeResults(prop); - return norm; - }, {}); - } - - return results; -}; diff --git a/src/endpoints/searchByIds/searchAllSources.ts b/src/endpoints/searchByIds/searchAllSources.ts deleted file mode 100644 index 2bd3212..0000000 --- a/src/endpoints/searchByIds/searchAllSources.ts +++ /dev/null @@ -1,40 +0,0 @@ -import { flatten } from 'lodash'; - -import { ArrangerProject } from '../../arrangerUtils'; -import { byBiospecimenId } from './byBiospecimenId'; -import { byFamilyId } from './byFamilyId'; -import { byId } from './byId'; -import { bySampleExternalId } from './bySampleExternalId'; -import executePagedQuery from './executePagedQuery'; -import { SearchByIdsResult, SourceType } from './searchByIdsTypes'; - -const searchSources = (sources: SourceType[]) => async ( - ids: string[], - projectId: string, - getProject: (projectId: string) => ArrangerProject, -) => { - const project = getProject(projectId); - if (!project) { - throw new Error(`ProjectID '${projectId}' cannot be established.`); - } - - const promises = sources.map(src => { - const sqon = src.getSqon(ids); - // get the data for this source - return ( - executePagedQuery(project, src.query, sqon) - // transform normalized data to a "query result" - .then((results: unknown) => src.transform(results, ids)) - // remove results without participants (id not found in this source) - .then((results: SearchByIdsResult[]) => results.filter(result => result.participantIds.length)) - ); - }); - - return await Promise.all(promises).then(flatten); -}; - -export const searchAllSources: ( - ids: string[], - projectId: string, - getProject: (projectId: string) => ArrangerProject, -) => Promise = searchSources([byId, byBiospecimenId, byFamilyId, bySampleExternalId]); diff --git a/src/endpoints/searchByIds/searchByIdsTypes.ts b/src/endpoints/searchByIds/searchByIdsTypes.ts deleted file mode 100644 index a151c0d..0000000 --- a/src/endpoints/searchByIds/searchByIdsTypes.ts +++ /dev/null @@ -1,13 +0,0 @@ -import { SetSqon } from '../sets/setsTypes'; - -export type SourceType = { - query: string; - getSqon: (ids: string[]) => SetSqon; - transform: (data: unknown, ids: string[]) => SearchByIdsResult[]; -}; - -export type SearchByIdsResult = { - search: string; - type: string; - participantIds: string[]; -}; diff --git a/src/endpoints/sets/setsFeature.test.ts b/src/endpoints/sets/setsFeature.test.ts deleted file mode 100644 index 5f4f08d..0000000 --- a/src/endpoints/sets/setsFeature.test.ts +++ /dev/null @@ -1,659 +0,0 @@ -import { SQS } from '@aws-sdk/client-sqs'; - -import { ArrangerProject } from '../../arrangerUtils'; -import { - CreateUpdateBody, - deleteRiff, - getRiffs, - Output as RiffOutput, - postRiff, - putRiff, - RIFF_TYPE_SET, -} from '../../riff/riffClient'; -import { resolveSetsInSqon } from '../../sqon/resolveSetInSqon'; -import { searchSqon } from '../../sqon/searchSqon'; -import { sendSetInSQSQueue } from '../../SQS/sendEvent'; -import { createSet, deleteSet, getSets, SubActionTypes, updateSetContent, updateSetTag } from './setsFeature'; -import { CreateSetBody, Set, Sort, UpdateSetContentBody, UpdateSetTagBody } from './setsTypes'; - -jest.mock('../../sqon/resolveSetInSqon'); -jest.mock('../../sqon/searchSqon'); -jest.mock('../../riff/riffClient'); -jest.mock('../../SQS/sendEvent'); -jest.mock('../../env', () => ({ - esHost: 'http://localhost:9200', - maxSetContentSize: 3, - sendUpdateToSqs: true, - PROJECT_INCLUDE: 'Include', - PROJECT_KIDSFIRST: 'KidsFirst', - project: 'KidsFirst', -})); - -describe('Set management', () => { - const sqon = { op: 'and', content: [] }; - const tag = 'tag'; - const idField = 'kf_id'; - const projectId = '2021_05_03_v2'; - const type = 'participant'; - const sort: Sort[] = []; - const accessToken = 'Bearer bearer'; - const setId = '1ea'; - const userId = 'user_id'; - const getProject = (_s: string) => ({} as ArrangerProject); - - const mockParticipantIds = ['participant_1', 'participant_2']; - - const riff: RiffOutput = { - id: setId, - alias: tag, - content: { - ids: mockParticipantIds, - sqon, - riffType: RIFF_TYPE_SET, - setType: type, - idField: 'fhir_id', - sort: [], - }, - sharedPublicly: false, - uid: 'abcedfghijkl', - creationDate: new Date(), - updatedDate: new Date(), - }; - - const setFromRiff: Set = { - id: setId, - tag, - size: mockParticipantIds.length, - setType: type, - updated_date: riff.updatedDate, - created_date: riff.creationDate, - }; - - describe('Get user sets using Riff API', () => { - beforeEach(() => { - (getRiffs as jest.Mock).mockReset(); - }); - - it('should send get riffs and return result filtered to keep only set with tag and convert to Set', async () => { - const mockUserRiffs = [riff, { ...riff, content: {} }, { ...riff, alias: '' }]; - const expectedSets: Set[] = [ - { - id: riff.id, - tag: riff.alias, - size: riff.content.ids.length, - setType: riff.content.setType, - created_date: riff.creationDate, - updated_date: riff.updatedDate, - }, - ]; - (getRiffs as jest.Mock).mockImplementation(() => mockUserRiffs); - - const result = await getSets(accessToken, userId); - - expect(result).toEqual(expectedSets); - expect((getRiffs as jest.Mock).mock.calls.length).toEqual(1); - }); - - it('should send get riffs and return error if get request throws an error', async () => { - (getRiffs as jest.Mock).mockImplementation(() => { - throw new Error('OOPS'); - }); - - try { - await getSets(accessToken, userId); - } catch (e) { - expect(e.message).toEqual('OOPS'); - } finally { - expect((getRiffs as jest.Mock).mock.calls.length).toEqual(1); - } - }); - }); - - describe('Create set using Riff API', () => { - const createSetBody: CreateSetBody = { - idField, - projectId, - sort, - sqon, - tag, - type, - }; - - const expectedCreateRiffBody: CreateUpdateBody = { - alias: tag, - sharedPublicly: false, - content: { - ids: mockParticipantIds, - idField, - sort, - sqon, - riffType: RIFF_TYPE_SET, - setType: type, - }, - }; - - const sqs = new SQS({ apiVersion: '2012-11-05' }); - - beforeEach(() => { - (resolveSetsInSqon as jest.Mock).mockReset(); - (searchSqon as jest.Mock).mockReset(); - (postRiff as jest.Mock).mockReset(); - (sendSetInSQSQueue as jest.Mock).mockReset(); - }); - - it('should send create riff, send message in SQS and return result', async () => { - (resolveSetsInSqon as jest.Mock).mockImplementation(sqon => sqon); - (sendSetInSQSQueue as jest.Mock).mockImplementation(() => Promise.resolve({ MessageId: '123' })); - (searchSqon as jest.Mock).mockImplementation(() => mockParticipantIds); - (postRiff as jest.Mock).mockImplementation(() => riff); - - const result = await createSet(createSetBody, accessToken, userId, sqs, getProject); - - expect(result).toEqual(setFromRiff); - expect((resolveSetsInSqon as jest.Mock).mock.calls.length).toEqual(1); - expect((searchSqon as jest.Mock).mock.calls.length).toEqual(1); - expect((postRiff as jest.Mock).mock.calls.length).toEqual(1); - expect((postRiff as jest.Mock).mock.calls[0][0]).toEqual(accessToken); - expect((postRiff as jest.Mock).mock.calls[0][1]).toEqual(expectedCreateRiffBody); - expect((sendSetInSQSQueue as jest.Mock).mock.calls.length).toEqual(1); - }); - - it('should resolve set_id in sqon before saving new set', async () => { - const sqonWithSetId = { - op: 'and', - content: [{ op: 'in', content: { field: 'kf_id', value: ['set_id:1a1'] } }], - }; - - const sqonWithResolvedSetId = { - op: 'and', - content: [{ op: 'in', content: { field: 'kf_id', value: mockParticipantIds } }], - }; - - (resolveSetsInSqon as jest.Mock).mockImplementation(() => sqonWithResolvedSetId); - (sendSetInSQSQueue as jest.Mock).mockImplementation(() => Promise.resolve({ MessageId: '123' })); - (searchSqon as jest.Mock).mockImplementation(() => mockParticipantIds); - (postRiff as jest.Mock).mockImplementation(() => riff); - - const result = await createSet( - { ...createSetBody, sqon: sqonWithSetId }, - accessToken, - userId, - sqs, - getProject, - ); - - expect(result).toEqual(setFromRiff); - expect((resolveSetsInSqon as jest.Mock).mock.calls.length).toEqual(1); - expect((resolveSetsInSqon as jest.Mock).mock.calls[0][0]).toEqual(sqonWithSetId); - expect((searchSqon as jest.Mock).mock.calls.length).toEqual(1); - expect((postRiff as jest.Mock).mock.calls.length).toEqual(1); - expect((postRiff as jest.Mock).mock.calls[0][0]).toEqual(accessToken); - expect((postRiff as jest.Mock).mock.calls[0][1]).toEqual({ - ...expectedCreateRiffBody, - content: { ...expectedCreateRiffBody.content, sqon: sqonWithSetId }, - }); - expect((sendSetInSQSQueue as jest.Mock).mock.calls.length).toEqual(1); - }); - - it('should truncate id list if greater than max defined in config', async () => { - const mockTooLongParticipantIds = [ - 'participant_1', - 'participant_2', - 'participant_3', - 'participant_4', - 'participant_5', - ]; - - const expectedRiff = { - ...riff, - content: { ...riff.content, ids: ['participant_1', 'participant_2', 'participant_3'] }, - }; - - const expectedSet = { - ...setFromRiff, - size: 3, - }; - - (resolveSetsInSqon as jest.Mock).mockImplementation(sqon => sqon); - (sendSetInSQSQueue as jest.Mock).mockImplementation(() => Promise.resolve({ MessageId: '123' })); - (searchSqon as jest.Mock).mockImplementation(() => mockTooLongParticipantIds); - (postRiff as jest.Mock).mockImplementation(() => expectedRiff); - - const result = await createSet(createSetBody, accessToken, userId, sqs, getProject); - - expect(result).toEqual(expectedSet); - expect((resolveSetsInSqon as jest.Mock).mock.calls.length).toEqual(1); - expect((searchSqon as jest.Mock).mock.calls.length).toEqual(1); - expect((postRiff as jest.Mock).mock.calls.length).toEqual(1); - expect((postRiff as jest.Mock).mock.calls[0][0]).toEqual(accessToken); - expect((postRiff as jest.Mock).mock.calls[0][1]).toEqual({ - ...expectedCreateRiffBody, - content: { - ...expectedCreateRiffBody.content, - ids: ['participant_1', 'participant_2', 'participant_3'], - }, - }); - expect((sendSetInSQSQueue as jest.Mock).mock.calls.length).toEqual(1); - }); - - it('should not send message in SQS for empty tag sets', async () => { - (resolveSetsInSqon as jest.Mock).mockImplementation(sqon => sqon); - (sendSetInSQSQueue as jest.Mock).mockImplementation(() => Promise.resolve({ MessageId: '123' })); - (searchSqon as jest.Mock).mockImplementation(() => mockParticipantIds); - (postRiff as jest.Mock).mockImplementation(() => ({ ...riff, alias: '' })); - - const result = await createSet({ ...createSetBody, tag: '' }, accessToken, userId, sqs, getProject); - - expect(result).toEqual({ ...setFromRiff, tag: '' }); - expect((resolveSetsInSqon as jest.Mock).mock.calls.length).toEqual(1); - expect((searchSqon as jest.Mock).mock.calls.length).toEqual(1); - expect((postRiff as jest.Mock).mock.calls.length).toEqual(1); - expect((sendSetInSQSQueue as jest.Mock).mock.calls.length).toEqual(0); - }); - - it('should send create riff and return error if creation request throws an error', async () => { - (resolveSetsInSqon as jest.Mock).mockImplementation(sqon => sqon); - (searchSqon as jest.Mock).mockImplementation(() => mockParticipantIds); - (postRiff as jest.Mock).mockImplementation(() => { - throw new Error('OOPS'); - }); - - try { - await createSet(createSetBody, accessToken, userId, sqs, getProject); - } catch (e) { - expect(e.message).toEqual('OOPS'); - } finally { - expect((resolveSetsInSqon as jest.Mock).mock.calls.length).toEqual(1); - expect((searchSqon as jest.Mock).mock.calls.length).toEqual(1); - expect((postRiff as jest.Mock).mock.calls.length).toEqual(1); - expect((postRiff as jest.Mock).mock.calls[0][0]).toEqual(accessToken); - expect((postRiff as jest.Mock).mock.calls[0][1]).toEqual(expectedCreateRiffBody); - expect((sendSetInSQSQueue as jest.Mock).mock.calls.length).toEqual(0); - } - }); - }); - - describe('Update set tag using Riff API', () => { - const updateSetTagBody: UpdateSetTagBody = { - newTag: 'tag updated', - sourceType: 'SAVE_SET', - subAction: SubActionTypes.RENAME_TAG, - }; - - const mockExistingSets = [riff]; - - const expectedUpdateRiffBody: CreateUpdateBody = { - alias: updateSetTagBody.newTag, - sharedPublicly: riff.sharedPublicly, - content: riff.content, - }; - - const updatedRiff: RiffOutput = { - ...riff, - alias: 'tag updated', - updatedDate: new Date(), - }; - - const sqs = new SQS({ apiVersion: '2012-11-05' }); - - beforeEach(() => { - (getRiffs as jest.Mock).mockReset(); - (putRiff as jest.Mock).mockReset(); - (sendSetInSQSQueue as jest.Mock).mockReset(); - }); - - it('should send put riff and return result', async () => { - const setFromUpdatedRiff: Set = { - ...setFromRiff, - tag: 'tag updated', - updated_date: updatedRiff.updatedDate, - }; - - (getRiffs as jest.Mock).mockImplementation(() => mockExistingSets); - (putRiff as jest.Mock).mockImplementation(() => updatedRiff); - (sendSetInSQSQueue as jest.Mock).mockImplementation(() => Promise.resolve({ MessageId: '123' })); - - const result = await updateSetTag(updateSetTagBody, accessToken, userId, setId, sqs); - - expect(result).toEqual(setFromUpdatedRiff); - expect((getRiffs as jest.Mock).mock.calls.length).toEqual(1); - expect((putRiff as jest.Mock).mock.calls.length).toEqual(1); - expect((putRiff as jest.Mock).mock.calls[0][0]).toEqual(accessToken); - expect((putRiff as jest.Mock).mock.calls[0][1]).toEqual(expectedUpdateRiffBody); - expect((putRiff as jest.Mock).mock.calls[0][2]).toEqual(setId); - expect((sendSetInSQSQueue as jest.Mock).mock.calls.length).toEqual(1); - }); - - it('should not send message in SQS for empty tag sets', async () => { - const setFromUpdatedRiff: Set = { ...setFromRiff, tag: '', updated_date: updatedRiff.updatedDate }; - - (getRiffs as jest.Mock).mockImplementation(() => mockExistingSets); - (putRiff as jest.Mock).mockImplementation(() => ({ ...updatedRiff, alias: '' })); - - const result = await updateSetTag({ ...updateSetTagBody, newTag: '' }, accessToken, userId, setId, sqs); - - expect(result).toEqual(setFromUpdatedRiff); - expect((getRiffs as jest.Mock).mock.calls.length).toEqual(1); - expect((putRiff as jest.Mock).mock.calls.length).toEqual(1); - expect((sendSetInSQSQueue as jest.Mock).mock.calls.length).toEqual(0); - }); - - it('should return an error if set to update does not exist', async () => { - (getRiffs as jest.Mock).mockImplementation(() => []); - (putRiff as jest.Mock).mockImplementation(() => updatedRiff); - - try { - await updateSetTag(updateSetTagBody, accessToken, userId, setId, sqs); - } catch (e) { - expect(e.message).toEqual('Set to update can not be found !'); - } finally { - expect((getRiffs as jest.Mock).mock.calls.length).toEqual(1); - expect((putRiff as jest.Mock).mock.calls.length).toEqual(0); - expect((sendSetInSQSQueue as jest.Mock).mock.calls.length).toEqual(0); - } - }); - - it('should send put riff and return error if update throws an error', async () => { - (getRiffs as jest.Mock).mockImplementation(() => mockExistingSets); - (putRiff as jest.Mock).mockImplementation(() => { - throw new Error('OOPS'); - }); - - try { - await updateSetTag(updateSetTagBody, accessToken, userId, setId, sqs); - } catch (e) { - expect(e.message).toEqual('OOPS'); - } finally { - expect((getRiffs as jest.Mock).mock.calls.length).toEqual(1); - expect((putRiff as jest.Mock).mock.calls.length).toEqual(1); - expect((putRiff as jest.Mock).mock.calls[0][0]).toEqual(accessToken); - expect((putRiff as jest.Mock).mock.calls[0][1]).toEqual(expectedUpdateRiffBody); - expect((putRiff as jest.Mock).mock.calls[0][2]).toEqual(setId); - expect((sendSetInSQSQueue as jest.Mock).mock.calls.length).toEqual(0); - } - }); - }); - - describe('Update set content using Riff API', () => { - const newSqon = { op: 'and', content: [{ op: 'in', content: { field: 'affected_status', value: ['false'] } }] }; - const mockNewSqonParticipantIds = ['participant_1', 'participant_3']; - - const mockExistingSets = [riff]; - - const updateSetContentAddSqon: UpdateSetContentBody = { - sourceType: 'SAVE_SET', - subAction: SubActionTypes.ADD_IDS, - projectId, - sqon: newSqon, - }; - - const updateSetContentRemoveSqon = { ...updateSetContentAddSqon, subAction: SubActionTypes.REMOVE_IDS }; - - const sqs = new SQS({ apiVersion: '2012-11-05' }); - - beforeEach(() => { - (getRiffs as jest.Mock).mockReset(); - (putRiff as jest.Mock).mockReset(); - (resolveSetsInSqon as jest.Mock).mockReset(); - (searchSqon as jest.Mock).mockReset(); - (sendSetInSQSQueue as jest.Mock).mockReset(); - }); - - it('should send put riff and return result - case add ids', async () => { - const expectedAddSqon = { op: 'or', content: [sqon, newSqon] }; - const updatedRiff = { - ...riff, - content: { - ...riff.content, - sqon: expectedAddSqon, - ids: ['participant_1', 'participant_2', 'participant_3'], - }, - updatedDate: new Date(), - }; - - const setFromUpdatedRiff: Set = { ...setFromRiff, size: 3, updated_date: updatedRiff.updatedDate }; - - const expectedUpdateRiffBody: CreateUpdateBody = { - alias: riff.alias, - sharedPublicly: riff.sharedPublicly, - content: { - ...riff.content, - sqon: expectedAddSqon, - ids: ['participant_1', 'participant_2', 'participant_3'], - }, - }; - - (getRiffs as jest.Mock).mockImplementation(() => mockExistingSets); - (resolveSetsInSqon as jest.Mock).mockImplementation(sqon => sqon); - (searchSqon as jest.Mock).mockImplementation(() => mockNewSqonParticipantIds); - (putRiff as jest.Mock).mockImplementation(() => updatedRiff); - (sendSetInSQSQueue as jest.Mock).mockImplementation(() => Promise.resolve({ MessageId: '123' })); - - const result = await updateSetContent(updateSetContentAddSqon, accessToken, userId, setId, sqs, getProject); - - expect(result).toEqual(setFromUpdatedRiff); - expect((getRiffs as jest.Mock).mock.calls.length).toEqual(1); - expect((resolveSetsInSqon as jest.Mock).mock.calls.length).toEqual(1); - expect((searchSqon as jest.Mock).mock.calls.length).toEqual(1); - expect((putRiff as jest.Mock).mock.calls.length).toEqual(1); - expect((putRiff as jest.Mock).mock.calls[0][0]).toEqual(accessToken); - expect((putRiff as jest.Mock).mock.calls[0][1]).toEqual(expectedUpdateRiffBody); - expect((putRiff as jest.Mock).mock.calls[0][2]).toEqual(setId); - expect((sendSetInSQSQueue as jest.Mock).mock.calls.length).toEqual(1); - }); - - it('should resolve set id in sqon before send put riff and return result - case add ids', async () => { - const newSqonWithSetId = { - op: 'and', - content: [{ op: 'in', content: { field: 'kf_id', value: ['set_id:1b1'] } }], - }; - const newSqonWithResolvedSet = { - op: 'and', - content: [{ op: 'in', content: { field: 'kf_id', value: mockNewSqonParticipantIds } }], - }; - const expectedAddSqon = { op: 'or', content: [sqon, newSqonWithSetId] }; - const updatedRiff = { - ...riff, - content: { - ...riff.content, - sqon: expectedAddSqon, - ids: ['participant_1', 'participant_2', 'participant_3'], - }, - updatedDate: new Date(), - }; - const setFromUpdatedRiff: Set = { ...setFromRiff, size: 3, updated_date: updatedRiff.updatedDate }; - - const expectedUpdateRiffBody: CreateUpdateBody = { - alias: riff.alias, - sharedPublicly: riff.sharedPublicly, - content: { - ...riff.content, - sqon: expectedAddSqon, - ids: ['participant_1', 'participant_2', 'participant_3'], - }, - }; - - (getRiffs as jest.Mock).mockImplementation(() => mockExistingSets); - (resolveSetsInSqon as jest.Mock).mockImplementation(() => newSqonWithResolvedSet); - (searchSqon as jest.Mock).mockImplementation(() => mockNewSqonParticipantIds); - (putRiff as jest.Mock).mockImplementation(() => updatedRiff); - (sendSetInSQSQueue as jest.Mock).mockImplementation(() => Promise.resolve({ MessageId: '123' })); - - const result = await updateSetContent( - { ...updateSetContentAddSqon, sqon: newSqonWithSetId }, - accessToken, - userId, - setId, - sqs, - getProject, - ); - - expect(result).toEqual(setFromUpdatedRiff); - expect((getRiffs as jest.Mock).mock.calls.length).toEqual(1); - expect((resolveSetsInSqon as jest.Mock).mock.calls.length).toEqual(1); - expect((resolveSetsInSqon as jest.Mock).mock.calls[0][0]).toEqual(newSqonWithSetId); - expect((searchSqon as jest.Mock).mock.calls.length).toEqual(1); - expect((searchSqon as jest.Mock).mock.calls[0][0]).toEqual(newSqonWithResolvedSet); - expect((putRiff as jest.Mock).mock.calls.length).toEqual(1); - expect((putRiff as jest.Mock).mock.calls[0][0]).toEqual(accessToken); - expect((putRiff as jest.Mock).mock.calls[0][1]).toEqual(expectedUpdateRiffBody); - expect((putRiff as jest.Mock).mock.calls[0][2]).toEqual(setId); - expect((sendSetInSQSQueue as jest.Mock).mock.calls.length).toEqual(1); - }); - - it('should not send message in SQS for empty tag sets', async () => { - const expectedAddSqon = { op: 'or', content: [sqon, newSqon] }; - const updatedRiff: RiffOutput = { - ...riff, - alias: '', - content: { - ...riff.content, - sqon: expectedAddSqon, - ids: ['participant_1', 'participant_2', 'participant_3'], - }, - updatedDate: new Date(), - }; - - const setFromUpdatedRiff: Set = { ...setFromRiff, size: 3, tag: '', updated_date: updatedRiff.updatedDate }; - - (getRiffs as jest.Mock).mockImplementation(() => [{ ...riff, tag: '' }]); - (resolveSetsInSqon as jest.Mock).mockImplementation(sqon => sqon); - (searchSqon as jest.Mock).mockImplementation(() => mockNewSqonParticipantIds); - (putRiff as jest.Mock).mockImplementation(() => updatedRiff); - - const result = await updateSetContent(updateSetContentAddSqon, accessToken, userId, setId, sqs, getProject); - - expect(result).toEqual(setFromUpdatedRiff); - expect((getRiffs as jest.Mock).mock.calls.length).toEqual(1); - expect((resolveSetsInSqon as jest.Mock).mock.calls.length).toEqual(1); - expect((searchSqon as jest.Mock).mock.calls.length).toEqual(1); - expect((putRiff as jest.Mock).mock.calls.length).toEqual(1); - expect((sendSetInSQSQueue as jest.Mock).mock.calls.length).toEqual(0); - }); - - it('should send put riff and return result - case remove ids', async () => { - const expectedRemoveSqon = { - op: 'and', - content: [sqon, { op: 'not', content: [newSqon] }], - }; - const updatedRiff = { - ...riff, - content: { - ...riff.content, - sqon: expectedRemoveSqon, - ids: ['participant_2'], - }, - updatedDate: new Date(), - }; - const setFromUpdatedRiff: Set = { ...setFromRiff, size: 1, updated_date: updatedRiff.updatedDate }; - - const expectedUpdateRiffBody: CreateUpdateBody = { - alias: riff.alias, - sharedPublicly: riff.sharedPublicly, - content: { - ...riff.content, - sqon: expectedRemoveSqon, - ids: ['participant_2'], - }, - }; - - (getRiffs as jest.Mock).mockImplementation(() => mockExistingSets); - (resolveSetsInSqon as jest.Mock).mockImplementation(sqon => sqon); - (searchSqon as jest.Mock).mockImplementation(() => mockNewSqonParticipantIds); - (putRiff as jest.Mock).mockImplementation(() => updatedRiff); - (sendSetInSQSQueue as jest.Mock).mockImplementation(() => Promise.resolve({ MessageId: '123' })); - - const result = await updateSetContent( - updateSetContentRemoveSqon, - accessToken, - userId, - setId, - sqs, - getProject, - ); - - expect(result).toEqual(setFromUpdatedRiff); - expect((getRiffs as jest.Mock).mock.calls.length).toEqual(1); - expect((resolveSetsInSqon as jest.Mock).mock.calls.length).toEqual(1); - expect((searchSqon as jest.Mock).mock.calls.length).toEqual(1); - expect((putRiff as jest.Mock).mock.calls.length).toEqual(1); - expect((putRiff as jest.Mock).mock.calls[0][0]).toEqual(accessToken); - expect((putRiff as jest.Mock).mock.calls[0][1]).toEqual(expectedUpdateRiffBody); - expect((putRiff as jest.Mock).mock.calls[0][2]).toEqual(setId); - expect((sendSetInSQSQueue as jest.Mock).mock.calls.length).toEqual(1); - }); - - it('should return an error if set to update does not exist', async () => { - (getRiffs as jest.Mock).mockImplementation(() => []); - - try { - await updateSetContent(updateSetContentAddSqon, accessToken, userId, setId, sqs, getProject); - } catch (e) { - expect(e.message).toEqual('Set to update can not be found !'); - } finally { - expect((getRiffs as jest.Mock).mock.calls.length).toEqual(1); - expect((resolveSetsInSqon as jest.Mock).mock.calls.length).toEqual(0); - expect((searchSqon as jest.Mock).mock.calls.length).toEqual(0); - expect((putRiff as jest.Mock).mock.calls.length).toEqual(0); - expect((sendSetInSQSQueue as jest.Mock).mock.calls.length).toEqual(0); - } - }); - - it('should send put riff and return error if update throws an error', async () => { - (getRiffs as jest.Mock).mockImplementation(() => mockExistingSets); - (resolveSetsInSqon as jest.Mock).mockImplementation(sqon => sqon); - (searchSqon as jest.Mock).mockImplementation(() => mockNewSqonParticipantIds); - (putRiff as jest.Mock).mockImplementation(() => { - throw new Error('OOPS'); - }); - - try { - await updateSetContent(updateSetContentAddSqon, accessToken, userId, setId, sqs, getProject); - } catch (e) { - expect(e.message).toEqual('OOPS'); - } finally { - expect((getRiffs as jest.Mock).mock.calls.length).toEqual(1); - expect((resolveSetsInSqon as jest.Mock).mock.calls.length).toEqual(1); - expect((searchSqon as jest.Mock).mock.calls.length).toEqual(1); - expect((putRiff as jest.Mock).mock.calls.length).toEqual(1); - expect((sendSetInSQSQueue as jest.Mock).mock.calls.length).toEqual(0); - } - }); - }); - - describe('Delete set using Riff API', () => { - const sqs = new SQS({ apiVersion: '2012-11-05' }); - - beforeEach(() => { - (searchSqon as jest.Mock).mockReset(); - (deleteRiff as jest.Mock).mockReset(); - (sendSetInSQSQueue as jest.Mock).mockReset(); - }); - - it('should send delete riff and return result', async () => { - (deleteRiff as jest.Mock).mockImplementation(() => true); - (sendSetInSQSQueue as jest.Mock).mockImplementation(() => Promise.resolve({ MessageId: '123' })); - - const result = await deleteSet(accessToken, setId, userId, sqs); - - expect(result).toEqual(true); - expect((deleteRiff as jest.Mock).mock.calls.length).toEqual(1); - expect((sendSetInSQSQueue as jest.Mock).mock.calls.length).toEqual(1); - }); - - it('should send delete riff and return error if delete throws an error', async () => { - (deleteRiff as jest.Mock).mockImplementation(() => { - throw new Error('OOPS'); - }); - - try { - await deleteSet(accessToken, setId, userId, sqs); - } catch (e) { - expect(e.message).toEqual('OOPS'); - } finally { - expect((deleteRiff as jest.Mock).mock.calls.length).toEqual(1); - expect((sendSetInSQSQueue as jest.Mock).mock.calls.length).toEqual(0); - } - }); - }); -}); diff --git a/src/endpoints/sets/setsFeature.ts b/src/endpoints/sets/setsFeature.ts index 065e7af..81e23b4 100644 --- a/src/endpoints/sets/setsFeature.ts +++ b/src/endpoints/sets/setsFeature.ts @@ -1,21 +1,10 @@ -import { SQSClient } from '@aws-sdk/client-sqs'; -import { difference, dropRight, get, union } from 'lodash'; +import { difference, dropRight, union } from 'lodash'; import { ArrangerProject } from '../../arrangerUtils'; -import { maxSetContentSize, project, PROJECT_INCLUDE, sendUpdateToSqs } from '../../env'; -import { - CreateUpdateBody, - deleteRiff, - getRiffs, - Output as RiffOutput, - postRiff, - putRiff, - RIFF_TYPE_SET, -} from '../../riff/riffClient'; +import { maxSetContentSize } from '../../env'; import { addSqonToSetSqon, removeSqonToSetSqon } from '../../sqon/manipulateSqon'; import { resolveSetsInSqon } from '../../sqon/resolveSetInSqon'; import { searchSqon } from '../../sqon/searchSqon'; -import { sendSetInSQSQueue } from '../../SQS/sendEvent'; import { deleteUserContent, getUserContents, @@ -26,30 +15,14 @@ import { import { SetNotFoundError } from './setError'; import { CreateSetBody, Set, UpdateSetContentBody, UpdateSetTagBody } from './setsTypes'; -const projectType = project; - export const SubActionTypes = { RENAME_TAG: 'RENAME_TAG', ADD_IDS: 'ADD_IDS', REMOVE_IDS: 'REMOVE_IDS', }; -const ActionTypes = { - CREATE: 'CREATE', - DELETE: 'DELETE', - UPDATE: 'UPDATE', -}; - -export const getUserSet = async (accessToken: string, userId: string, setId: string): Promise => { - let existingSetsFilterById: UserSetOutput[]; - if (projectType === PROJECT_INCLUDE) { - existingSetsFilterById = (await getUserContents(accessToken)).filter(r => r.id === setId); - } else { - existingSetsFilterById = (await getRiffs(accessToken, userId)) - .filter(r => r.id === setId) - .map(s => mapRiffOutputToUserOutput(s)); - } - +export const getUserSet = async (accessToken: string, setId: string): Promise => { + const existingSetsFilterById: UserSetOutput[] = (await getUserContents(accessToken)).filter(r => r.id === setId); if (existingSetsFilterById.length !== 1) { throw new SetNotFoundError('Set to update can not be found !'); } @@ -57,25 +30,15 @@ export const getUserSet = async (accessToken: string, userId: string, setId: str return existingSetsFilterById[0]; }; -export const getSets = async (accessToken: string, userId: string): Promise => { - if (projectType === PROJECT_INCLUDE) { - const userContents = await getUserContents(accessToken); - - return userContents.map(set => mapUserResultToSet(set)); - } else { - const userContents = await getRiffs(accessToken, userId); - return userContents - .filter(riff => get(riff, 'content.riffType', '') === RIFF_TYPE_SET) - .filter(riff => riff.alias) - .map(riff => mapRiffResultToSet(riff)); - } +export const getSets = async (accessToken: string): Promise => { + const userContents = await getUserContents(accessToken); + return userContents.map(set => mapUserResultToSet(set)); }; export const createSet = async ( requestBody: CreateSetBody, accessToken: string, userId: string, - sqs: SQSClient, getProject: (projectId: string) => ArrangerProject, ): Promise => { const { sqon, sort, projectId, type, idField, tag } = requestBody; @@ -84,76 +47,30 @@ export const createSet = async ( const truncatedIds = truncateIds(ids); - const payload: CreateUpdateBody = { + const payload = { alias: tag, sharedPublicly: false, - content: { ids: truncatedIds, riffType: RIFF_TYPE_SET, setType: type, sqon, sort, idField }, + content: { ids: truncatedIds, setType: type, sqon, sort, idField }, }; - let setResult: Set; - if (projectType === PROJECT_INCLUDE) { - if (!payload.alias || !payload.content.ids) { - throw Error(`Set must have ${!payload.alias ? 'a name' : 'no set ids'}`); - } - const createResult = await postUserContent(accessToken, payload); - setResult = mapUserResultToSet(createResult); - } else { - const createResult = await postRiff(accessToken, payload); - setResult = mapRiffResultToSet(createResult); - } - - if (sendUpdateToSqs && setResult.tag) { - await sendSetInSQSQueue(sqs, { - actionType: ActionTypes.CREATE, - values: { - userId, - setId: setResult.id, - ids: truncatedIds, - size: truncatedIds.length, - sqon, - path: idField, - type, - tag, - createdAt: setResult.created_date, - }, - }); + if (!payload.alias || !payload.content.ids) { + throw Error(`Set must have ${!payload.alias ? 'a name' : 'no set ids'}`); } - return setResult; + const createResult = await postUserContent(accessToken, payload); + return mapUserResultToSet(createResult); }; -export const updateSetTag = async ( - requestBody: UpdateSetTagBody, - accessToken: string, - userId: string, - setId: string, - sqs: SQSClient, -): Promise => { - const setToUpdate: UserSetOutput = await getUserSet(accessToken, userId, setId); +export const updateSetTag = async (requestBody: UpdateSetTagBody, accessToken: string, setId: string): Promise => { + const setToUpdate: UserSetOutput = await getUserSet(accessToken, setId); - const payload: CreateUpdateBody = { + const payload = { alias: requestBody.newTag, sharedPublicly: setToUpdate.sharedpublicly, content: setToUpdate.content, }; - let setResult: Set; - if (projectType === PROJECT_INCLUDE) { - const updateResult = await putUserContent(accessToken, payload, setId); - setResult = mapUserResultToSet(updateResult); - } else { - const updateResult = await putRiff(accessToken, payload, setId); - setResult = mapRiffResultToSet(updateResult); - } - - if (sendUpdateToSqs && setResult.tag) { - await sendSetInSQSQueue(sqs, { - actionType: ActionTypes.UPDATE, - subActionType: requestBody.subAction, - values: { userId, setId, newTag: setResult.tag }, - }); - } - - return setResult; + const updateResult = await putUserContent(accessToken, payload, setId); + return mapUserResultToSet(updateResult); }; export const updateSetContent = async ( @@ -161,10 +78,9 @@ export const updateSetContent = async ( accessToken: string, userId: string, setId: string, - sqs: SQSClient, getProject: (projectId: string) => ArrangerProject, ): Promise => { - const setToUpdate = await getUserSet(accessToken, userId, setId); + const setToUpdate = await getUserSet(accessToken, setId); const { sqon, ids, setType } = setToUpdate.content; @@ -192,59 +108,20 @@ export const updateSetContent = async ( requestBody.subAction === SubActionTypes.ADD_IDS ? union(ids, newSqonIds) : difference(ids, newSqonIds); const truncatedIds = truncateIds(existingIdsWithNewIds); - const payload: CreateUpdateBody = { + const payload = { alias: setToUpdate.alias, sharedPublicly: setToUpdate.sharedpublicly, content: { ...setToUpdate.content, sqon: existingSqonWithNewSqon, ids: truncatedIds }, }; - let setResult: Set; - if (projectType === PROJECT_INCLUDE) { - const updateResult = await putUserContent(accessToken, payload, setId); - setResult = mapUserResultToSet(updateResult); - } else { - const updateResult = await putRiff(accessToken, payload, setId); - setResult = mapRiffResultToSet(updateResult); - } - - if (sendUpdateToSqs && setResult.tag) { - await sendSetInSQSQueue(sqs, { - actionType: ActionTypes.UPDATE, - subActionType: requestBody.subAction, - values: { - userId, - setId, - tag: setResult.tag, - ids: truncatedIds, - createdAt: setResult.created_date, - }, - }); - } - return setResult; + const updateResult = await putUserContent(accessToken, payload, setId); + return mapUserResultToSet(updateResult); }; export const deleteSet = async ( accessToken: string, - setId: string, - userId: string, - sqs: SQSClient, -): Promise => { - let deleteResult; - - if (projectType === PROJECT_INCLUDE) { - deleteResult = await deleteUserContent(accessToken, setId); - } else { - deleteResult = await deleteRiff(accessToken, setId); - } - - if (sendUpdateToSqs) { - await sendSetInSQSQueue(sqs, { - actionType: ActionTypes.DELETE, - values: { setIds: [setId], userId }, - }); - } - return deleteResult; -}; + setId: string +): Promise => await deleteUserContent(accessToken, setId); const mapUserResultToSet = (output: UserSetOutput): Set => ({ id: output.id, @@ -255,25 +132,6 @@ const mapUserResultToSet = (output: UserSetOutput): Set => ({ created_date: output.creation_date, }); -const mapRiffResultToSet = (output: RiffOutput): Set => ({ - id: output.id, - tag: output.alias, - size: output.content.ids.length, - updated_date: output.updatedDate, - setType: output.content.setType, - created_date: output.creationDate, -}); - -export const mapRiffOutputToUserOutput = (output: RiffOutput): UserSetOutput => ({ - id: output.id, - keycloak_id: output.uid, - content: output.content, - alias: output.alias, - sharedpublicly: output.sharedPublicly, - creation_date: output.creationDate, - updated_date: output.updatedDate, -}); - const truncateIds = (ids: string[]): string[] => { if (ids.length <= maxSetContentSize) { return ids; diff --git a/src/endpoints/statistics/includeBiospecimen.ts b/src/endpoints/statistics/includeBiospecimen.ts deleted file mode 100644 index 25abce6..0000000 --- a/src/endpoints/statistics/includeBiospecimen.ts +++ /dev/null @@ -1,14 +0,0 @@ -import { Client } from '@elastic/elasticsearch'; - -import { biospecimenIdKey, esBiospecimenIndex } from '../../env'; - -export const fetchBiospecimenStats = async (client: Client): Promise => { - const { body } = await client.search({ - index: esBiospecimenIndex, - body: { - aggs: { types_count: { value_count: { field: biospecimenIdKey } } }, - }, - size: 0, - }); - return body.aggregations.types_count.value; -}; diff --git a/src/endpoints/statistics/index.ts b/src/endpoints/statistics/index.ts index eaa6779..16708fa 100644 --- a/src/endpoints/statistics/index.ts +++ b/src/endpoints/statistics/index.ts @@ -3,6 +3,8 @@ import filesize from 'filesize'; import EsInstance from '../../ElasticSearchClientInstance'; import { + biospecimenIdKey, + esBiospecimenIndex, esFileIndex, esParticipantIndex, esStudyIndex, @@ -10,13 +12,8 @@ import { familyIdKey, fileIdKey, participantIdKey, - project, - PROJECT_INCLUDE, - PROJECT_KIDSFIRST, studyIdKey, } from '../../env'; -import { fetchBiospecimenStats as fetchIncludeBiospecimen } from './includeBiospecimen'; -import { fetchBiospecimenStats as fetchKidsfirstBiospecimen } from './kidsfirstBiospecimen'; export type Diagnosis = { mondo_id: string; @@ -101,15 +98,14 @@ const fetchFamilyStats = async (client: Client): Promise => { }; const fetchBiospecimenStats = async (client: Client): Promise => { - if (project === PROJECT_KIDSFIRST) { - return fetchKidsfirstBiospecimen(client); - } - - if (project === PROJECT_INCLUDE) { - return fetchIncludeBiospecimen(client); - } - - return Promise.resolve(0); + const { body } = await client.search({ + index: esBiospecimenIndex, + body: { + aggs: { types_count: { value_count: { field: biospecimenIdKey } } }, + }, + size: 0, + }); + return body.aggregations.types_count.value; }; export const fetchVariantStats = async (client: Client): Promise => { diff --git a/src/endpoints/statistics/kidsfirstBiospecimen.ts b/src/endpoints/statistics/kidsfirstBiospecimen.ts deleted file mode 100644 index 504ab45..0000000 --- a/src/endpoints/statistics/kidsfirstBiospecimen.ts +++ /dev/null @@ -1,19 +0,0 @@ -import { Client } from '@elastic/elasticsearch'; - -import { biospecimenIdKey, esParticipantIndex } from '../../env'; - -export const fetchBiospecimenStats = async (client: Client): Promise => { - const { body } = await client.search({ - index: esParticipantIndex, - body: { - aggs: { - list: { - nested: { path: 'biospecimens' }, - aggs: { types_count: { value_count: { field: `biospecimens.${biospecimenIdKey}` } } }, - }, - }, - }, - size: 0, - }); - return body.aggregations.list.doc_count; -}; diff --git a/src/env.ts b/src/env.ts index 211646b..6b1bd15 100644 --- a/src/env.ts +++ b/src/env.ts @@ -2,10 +2,10 @@ import dotenv from 'dotenv'; dotenv.config(); -export const PROJECT_KIDSFIRST = 'KidsFirst'; -export const PROJECT_INCLUDE = 'Include'; +//TODO DELETE in confs //export const PROJECT_KIDSFIRST = 'KidsFirst'; +//TODO DELETE in confs //export const PROJECT_INCLUDE = 'Include'; -export const project = process.env.PROJECT || PROJECT_KIDSFIRST; +//TODO DELETE in confs //export const project = process.env.PROJECT || PROJECT_KIDSFIRST; export const port = process.env.PORT || 5050; export const keycloakURL = process.env.KEYCLOAK_URL || 'https://kf-keycloak-qa.kf-strides.org/auth'; @@ -28,11 +28,12 @@ export const maxNOfGenomicFeatureSuggestions = process.env.MAX_NUMBER_OF_GF_SUGG export const indexNameGeneFeatureSuggestion = process.env.GENES_SUGGESTIONS_INDEX_NAME; export const indexNameVariantFeatureSuggestion = process.env.VARIANTS_SUGGESTIONS_INDEX_NAME; -export const riffURL = process.env.RIFF_URL || 'https://riff-qa.kf-strides.org'; +//TODO DELETE in confs //export const riffURL = process.env.RIFF_URL || 'https://riff-qa.kf-strides.org'; export const userApiURL = process.env.USER_API_URL || 'https://include-users-api-qa.373997854230.d3b.io'; -export const sendUpdateToSqs = process.env.SEND_UPDATE_TO_SQS !== 'false'; -export const sqsQueueUrl = process.env.SQS_QUEUE_URL || ''; +//TODO DELETE in confs //export const sendUpdateToSqs = process.env.SEND_UPDATE_TO_SQS !== 'false'; +//TODO DELETE in confs //export const sqsQueueUrl = process.env.SQS_QUEUE_URL || ''; export const maxSetContentSize: number = Number.parseInt(process.env.MAX_SET_CONTENT_SIZE) || 100000; +//TODO change default values export const idKey = process.env.ID_KEY || 'kf_id'; export const fileIdKey = process.env.FILE_ID_KEY || 'kf_id'; export const studyIdKey = process.env.STUDY_ID_KEY || 'kf_id'; diff --git a/src/index.ts b/src/index.ts index b46a7bd..df3bdf8 100644 --- a/src/index.ts +++ b/src/index.ts @@ -3,7 +3,6 @@ import 'regenerator-runtime/runtime.js'; import Arranger from '@arranger/server'; import { getProject } from '@arranger/server'; -import { SQSClient } from '@aws-sdk/client-sqs'; import Keycloak from 'keycloak-connect'; import buildApp from './app'; @@ -27,8 +26,7 @@ process.on('SIGINT', () => { const keycloak = new Keycloak({}, keycloakConfig); -const sqs = new SQSClient({}); -const app = buildApp(keycloak, sqs, getProject); +const app = buildApp(keycloak, getProject); const externalContext = (req, _res, _con) => ({ auth: req.kauth?.grant?.access_token || {} }); Arranger({ diff --git a/src/riff/riffClient.test.ts b/src/riff/riffClient.test.ts deleted file mode 100644 index 4027c97..0000000 --- a/src/riff/riffClient.test.ts +++ /dev/null @@ -1,185 +0,0 @@ -import fetch from 'node-fetch'; - -import { CreateUpdateBody, deleteRiff, getRiffs, postRiff, putRiff, Output, Content } from '../riff/riffClient'; -import { RiffError } from './riffError'; - -jest.mock('node-fetch'); - -describe('Riff Client', () => { - const accessToken = 'Bearer bearer'; - const userId = 'user_id'; - const setId = '1ea'; - - const createUpdateRiffPayload = { - alias: 'tag', - content: {}, - sharedPublicly: false, - } as CreateUpdateBody; - - const riff = { - id: setId, - uid: 'abcedfghijkl', - content: {} as Content, - alias: 'tag', - sharedPublicly: false, - creationDate: new Date(), - updatedDate: new Date(), - } as Output; - - describe('Get user riffs', () => { - beforeEach(() => { - ((fetch as unknown) as jest.Mock).mockReset(); - }); - - it('should return body if status is 200', async () => { - const mockResponse = { status: 200, json: () => [riff, riff] }; - ((fetch as unknown) as jest.Mock).mockImplementation(() => mockResponse); - - const result = await getRiffs(accessToken, userId); - - expect(result).toEqual([riff, riff]); - expect(((fetch as unknown) as jest.Mock).mock.calls.length).toEqual(1); - }); - - it('should throw a RiffError if status is not 200', async () => { - const expectedUnauthorized = { - timestamp: '2021-09-24T15:12:06.959+00:00', - status: 401, - error: 'Unauthorized', - message: '', - path: '/riff/user_id', - }; - - const expectedError = new RiffError(400, expectedUnauthorized); - const mockResponse = { status: 400, json: () => expectedUnauthorized }; - - ((fetch as unknown) as jest.Mock).mockImplementation(() => mockResponse); - - try { - await getRiffs(accessToken, userId); - } catch (e) { - expect(e).toEqual(expectedError); - } finally { - expect(((fetch as unknown) as jest.Mock).mock.calls.length).toEqual(1); - } - }); - }); - - describe('Post riff', () => { - beforeEach(() => { - ((fetch as unknown) as jest.Mock).mockReset(); - }); - - it('should return body if status is 200', async () => { - const mockResponse = { status: 200, json: () => riff }; - ((fetch as unknown) as jest.Mock).mockImplementation(() => mockResponse); - - const result = await postRiff(accessToken, createUpdateRiffPayload); - - expect(result).toEqual(riff); - expect(((fetch as unknown) as jest.Mock).mock.calls.length).toEqual(1); - }); - - it('should throw a RiffError if status is not 200', async () => { - const expectedBadRequest = { - timestamp: '2021-09-24T15:08:44.482+00:00', - status: 400, - error: 'Bad Request', - message: '', - path: '/riff/shorten', - }; - - const expectedError = new RiffError(400, expectedBadRequest); - const mockResponse = { status: 400, json: () => expectedBadRequest }; - - ((fetch as unknown) as jest.Mock).mockImplementation(() => mockResponse); - - try { - await postRiff(accessToken, createUpdateRiffPayload); - } catch (e) { - expect(e).toEqual(expectedError); - } finally { - expect(((fetch as unknown) as jest.Mock).mock.calls.length).toEqual(1); - } - }); - }); - - describe('Put riff', () => { - beforeEach(() => { - ((fetch as unknown) as jest.Mock).mockReset(); - }); - - it('should return body if status is 200', async () => { - const updateRiff = { ...riff, alias: 'tag updated', updatedDate: new Date() }; - const mockResponse = { status: 200, json: () => updateRiff }; - ((fetch as unknown) as jest.Mock).mockImplementation(() => mockResponse); - - const result = await putRiff(accessToken, { ...createUpdateRiffPayload, alias: 'tag updated' }, setId); - - expect(result).toEqual(updateRiff); - expect(((fetch as unknown) as jest.Mock).mock.calls.length).toEqual(1); - }); - - it('should throw a RiffError if status is not 200', async () => { - const expectedNotFound = { - timestamp: '2021-09-24T15:41:35.842+00:00', - status: 404, - error: 'Not Found', - message: '', - path: '/riff/1ea', - }; - - const expectedError = new RiffError(404, expectedNotFound); - const mockResponse = { status: 404, json: () => expectedNotFound }; - - ((fetch as unknown) as jest.Mock).mockImplementation(() => mockResponse); - - try { - await putRiff(accessToken, { ...createUpdateRiffPayload, alias: 'tag updated' }, setId); - } catch (e) { - expect(e).toEqual(expectedError); - } finally { - expect(((fetch as unknown) as jest.Mock).mock.calls.length).toEqual(1); - } - }); - }); - - describe('Delete riff', () => { - beforeEach(() => { - ((fetch as unknown) as jest.Mock).mockReset(); - }); - - it('should return body if status is 200', async () => { - const mockResponse = { status: 200, json: () => true }; - ((fetch as unknown) as jest.Mock).mockImplementation(() => mockResponse); - - const result = await deleteRiff(accessToken, setId); - - expect(result).toEqual(true); - expect(((fetch as unknown) as jest.Mock).mock.calls.length).toEqual(1); - }); - - it('should throw a RiffError if status is not 200', async () => { - const expectedUnauthorized = { - timestamp: '2021-09-24T15:12:06.959+00:00', - status: 401, - error: 'Unauthorized', - message: '', - path: '/riff/1ea', - }; - - const expectedError = new RiffError(401, expectedUnauthorized); - const mockResponse = { status: 401, json: () => expectedUnauthorized }; - - ((fetch as unknown) as jest.Mock).mockImplementation(() => mockResponse); - - try { - await deleteRiff(accessToken, setId); - } catch (e) { - expect(e).toEqual(expectedError); - } finally { - expect(((fetch as unknown) as jest.Mock).mock.calls.length).toEqual(1); - } - }); - }); -}); diff --git a/src/riff/riffClient.ts b/src/riff/riffClient.ts deleted file mode 100644 index e65e770..0000000 --- a/src/riff/riffClient.ts +++ /dev/null @@ -1,114 +0,0 @@ -import fetch from 'node-fetch'; - -import { SetSqon, Sort } from '../endpoints/sets/setsTypes'; -import { riffURL } from '../env'; -import { RiffError } from './riffError'; - -export const RIFF_TYPE_SET = 'set'; - -export type CreateUpdateBody = { - alias: string; - content: Content; - sharedPublicly: boolean; -}; - -export type Content = { - setType: string; - riffType: string; - ids: string[]; - sqon: SetSqon; - sort: Sort[]; - idField: string; -}; - -export type Output = { - id: string; - uid: string; - content: Content; - alias: string; - sharedPublicly: boolean; - creationDate: Date; - updatedDate: Date; -}; - -export const getRiffs = async (accessToken: string, userId: string): Promise => { - const uri = `${riffURL}/riff/user/${userId}`; - - const response = await fetch(encodeURI(uri), { - method: 'get', - headers: { - Authorization: accessToken, - 'Content-Type': 'application/json', - }, - }); - - const body = await response.json(); - - if (response.status === 200) { - return body; - } - - throw new RiffError(response.status, body); -}; - -export const postRiff = async (accessToken: string, set: CreateUpdateBody): Promise => { - const uri = `${riffURL}/riff/shorten`; - - const response = await fetch(encodeURI(uri), { - method: 'post', - headers: { - Authorization: accessToken, - 'Content-Type': 'application/json', - }, - body: JSON.stringify(set), - }); - - const body = await response.json(); - - if (response.status === 200) { - return body; - } - - throw new RiffError(response.status, body); -}; - -export const putRiff = async (accessToken: string, set: CreateUpdateBody, setId: string): Promise => { - const uri = `${riffURL}/riff/${setId}`; - - const response = await fetch(encodeURI(uri), { - method: 'put', - headers: { - Authorization: accessToken, - 'Content-Type': 'application/json', - }, - body: JSON.stringify(set), - }); - - const body = await response.json(); - - if (response.status === 200) { - return body; - } - - throw new RiffError(response.status, body); -}; - -export const deleteRiff = async (accessToken: string, setId: string): Promise => { - const uri = `${riffURL}/riff/${setId}`; - - const response = await fetch(encodeURI(uri), { - method: 'delete', - headers: { - Authorization: accessToken, - 'Content-Type': 'application/json', - }, - }); - - const body = await response.json(); - - if (response.status === 200) { - return body; - } - - throw new RiffError(response.status, body); -}; diff --git a/src/riff/riffError.ts b/src/riff/riffError.ts deleted file mode 100644 index c946b30..0000000 --- a/src/riff/riffError.ts +++ /dev/null @@ -1,12 +0,0 @@ -export class RiffError extends Error { - public readonly status: number; - public readonly details: unknown; - - constructor(status: number, details: unknown) { - super(`Riff returns status ${status}`); - Object.setPrototypeOf(this, RiffError.prototype); - this.name = RiffError.name; - this.status = status; - this.details = details; - } -} diff --git a/src/sqon/resolveSetInSqon.test.ts b/src/sqon/resolveSetInSqon.test.ts index 988563c..358a341 100644 --- a/src/sqon/resolveSetInSqon.test.ts +++ b/src/sqon/resolveSetInSqon.test.ts @@ -1,234 +1,14 @@ /* eslint-disable @typescript-eslint/no-var-requires */ -import { SetSqon } from '../endpoints/sets/setsTypes'; -import { getRiffs, Output as RiffOutput, RIFF_TYPE_SET } from '../riff/riffClient'; + import { getSharedSet, getUserContents, Output as UserSetOutput } from '../userApi/userApiClient'; -import { resolveSetsInSqon, retrieveSetsFromUsers } from './resolveSetInSqon'; +import { retrieveSetsFromUsers } from './resolveSetInSqon'; -jest.mock('../riff/riffClient'); jest.mock('../userApi/userApiClient'); -jest.mock('../env'); - -describe('resolveSetsInSqon - legacy KF', () => { - beforeEach(() => { - (getRiffs as jest.Mock).mockReset(); - const env = require('../env'); - env.project = 'Kidsfirst'; - }); - - it('should return the input sqon if not set id in it', async () => { - const inputSqonWithoutSetId: SetSqon = { - op: 'and', - content: [ - { - op: 'in', - content: { - field: 'gender', - value: ['Female'], - }, - }, - ], - }; - - const result = await resolveSetsInSqon(inputSqonWithoutSetId, 'userId', 'access_token'); - - expect(result).toEqual(inputSqonWithoutSetId); - expect((getRiffs as jest.Mock).mock.calls.length).toEqual(0); - }); - - it('should replace set id by its content', async () => { - const inputSqonWithSetIds: SetSqon = { - op: 'and', - content: [ - { - op: 'in', - content: { - field: 'kf_id', - value: ['set_id:1ez'], - }, - }, - { - op: 'in', - content: { - field: 'kf_id', - value: ['set_id:1ey'], - }, - }, - ], - }; - - const riff1ez: RiffOutput = { - id: '1ez', - alias: 'tag-1ez', - content: { - ids: ['participant_1', 'participant_2'], - sqon: { op: 'and', content: [] }, - riffType: RIFF_TYPE_SET, - setType: 'participant', - idField: 'fhir_id', - sort: [], - }, - sharedPublicly: false, - uid: 'uid-1ez', - creationDate: new Date(), - updatedDate: new Date(), - }; - - const riff1ey: RiffOutput = { - id: '1ey', - alias: 'tag-1ey', - content: { - ids: ['participant_1', 'participant_3'], - sqon: { op: 'and', content: [] }, - riffType: RIFF_TYPE_SET, - setType: 'participant', - idField: 'fhir_id', - sort: [], - }, - sharedPublicly: false, - uid: 'uid-1ey', - creationDate: new Date(), - updatedDate: new Date(), - }; - - const anotherRiff: RiffOutput = { - id: '1ea', - alias: 'tag-1ea', - content: { - ids: ['participant_2', 'participant_3'], - sqon: { op: 'and', content: [] }, - riffType: RIFF_TYPE_SET, - setType: 'participant', - idField: 'fhir_id', - sort: [], - }, - sharedPublicly: false, - uid: 'uid-1ea', - creationDate: new Date(), - updatedDate: new Date(), - }; - - const getRiffsMockResponse = [riff1ey, anotherRiff, riff1ez]; - - (getRiffs as jest.Mock).mockImplementation(() => getRiffsMockResponse); - - const expectedResult: SetSqon = { - op: 'and', - content: [ - { - op: 'in', - content: { - field: 'kf_id', - value: ['participant_1', 'participant_2'], - }, - }, - { - op: 'in', - content: { - field: 'kf_id', - value: ['participant_1', 'participant_3'], - }, - }, - ], - }; - - const result = await resolveSetsInSqon(inputSqonWithSetIds, 'userId', 'access_token'); - - expect(result).toEqual(expectedResult); - expect((getRiffs as jest.Mock).mock.calls.length).toEqual(1); - }); - - it('should replace set id by an empty array if it has not any set content matching to it', async () => { - const inputSqonWithSetIds: SetSqon = { - op: 'and', - content: [ - { - op: 'in', - content: { - field: 'kf_id', - value: ['set_id:1ez'], - }, - }, - { - op: 'in', - content: { - field: 'kf_id', - value: ['set_id:1ex'], - }, - }, - ], - }; - - const riff1ez: RiffOutput = { - id: '1ez', - alias: 'tag-1ez', - content: { - ids: ['participant_1', 'participant_2'], - sqon: { op: 'and', content: [] }, - riffType: RIFF_TYPE_SET, - setType: 'participant', - idField: 'fhir_id', - sort: [], - }, - sharedPublicly: false, - uid: 'uid-1ez', - creationDate: new Date(), - updatedDate: new Date(), - }; - - const anotherRiff: RiffOutput = { - id: '1ea', - alias: 'tag-1ea', - content: { - ids: ['participant_2', 'participant_3'], - sqon: { op: 'and', content: [] }, - riffType: RIFF_TYPE_SET, - setType: 'participant', - idField: 'fhir_id', - sort: [], - }, - sharedPublicly: false, - uid: 'uid-1ea', - creationDate: new Date(), - updatedDate: new Date(), - }; - - const getRiffsMockResponse = [anotherRiff, riff1ez]; - - (getRiffs as jest.Mock).mockImplementation(() => getRiffsMockResponse); - - const expectedResult: SetSqon = { - op: 'and', - content: [ - { - op: 'in', - content: { - field: 'kf_id', - value: ['participant_1', 'participant_2'], - }, - }, - { - op: 'in', - content: { - field: 'kf_id', - value: [], - }, - }, - ], - }; - - const result = await resolveSetsInSqon(inputSqonWithSetIds, 'userId', 'access_token'); - - expect(result).toEqual(expectedResult); - expect((getRiffs as jest.Mock).mock.calls.length).toEqual(1); - }); -}); describe('retrieveSetsFromUsers', () => { beforeEach(() => { (getUserContents as jest.Mock).mockReset(); (getSharedSet as jest.Mock).mockReset(); - const env = require('../env'); - env.project = 'Include'; }); const setIds = ['setId1', 'setId2']; @@ -240,7 +20,6 @@ describe('retrieveSetsFromUsers', () => { sqon: { op: 'and', content: [] }, idField: 'fhir_id', sort: [], - riffType: RIFF_TYPE_SET, setType: 'participant', }, sharedpublicly: false, @@ -256,7 +35,6 @@ describe('retrieveSetsFromUsers', () => { sqon: { op: 'and', content: [] }, idField: 'fhir_id', sort: [], - riffType: RIFF_TYPE_SET, setType: 'participant', }, sharedpublicly: false, @@ -272,7 +50,6 @@ describe('retrieveSetsFromUsers', () => { sqon: { op: 'and', content: [] }, idField: 'fhir_id', sort: [], - riffType: RIFF_TYPE_SET, setType: 'participant', }, sharedpublicly: true, diff --git a/src/sqon/resolveSetInSqon.ts b/src/sqon/resolveSetInSqon.ts index 5887755..c54e589 100644 --- a/src/sqon/resolveSetInSqon.ts +++ b/src/sqon/resolveSetInSqon.ts @@ -1,9 +1,6 @@ import { Dictionary, flattenDeep, get, isArray, zipObject } from 'lodash'; -import { mapRiffOutputToUserOutput } from '../endpoints/sets/setsFeature'; import { SetSqon } from '../endpoints/sets/setsTypes'; -import { project, PROJECT_INCLUDE } from '../env'; -import { getRiffs } from '../riff/riffClient'; import { getSharedSet, getUserContents, Output as UserSetOutput } from '../userApi/userApiClient'; const getSetIdsFromSqon = (sqon: SetSqon, collection = []) => @@ -34,13 +31,7 @@ const injectIdsIntoSqon = (sqon: SetSqon, setIdsToValueMap: Dictionary export const resolveSetsInSqon = async (sqon: SetSqon, userId: string, accessToken: string): Promise => { const setIds: string[] = getSetIdsFromSqon(sqon || ({} as SetSqon)); if (setIds.length) { - let userSets: UserSetOutput[]; - if (project === PROJECT_INCLUDE) { - userSets = await retrieveSetsFromUsers(accessToken, setIds); - } else { - userSets = (await getRiffs(accessToken, userId)).map(s => mapRiffOutputToUserOutput(s)); - } - + const userSets: UserSetOutput[] = await retrieveSetsFromUsers(accessToken, setIds); const ids = setIds.map(setId => get(userSets.filter(r => r.id === setId)[0], 'content.ids', [])); const setIdsToValueMap: Dictionary = zipObject( setIds.map(id => `set_id:${id}`), diff --git a/src/sqon/setSqon.ts b/src/sqon/setSqon.ts index ac4f653..5f39e4e 100644 --- a/src/sqon/setSqon.ts +++ b/src/sqon/setSqon.ts @@ -15,7 +15,7 @@ const getPathToParticipantId = (type: string) => { }; const CAPTURING_GROUP_OF_SET_ID_VALUE = 1; -export const replaceSetByIds = async (sqon: SetSqon, accessToken: string, userId: string): Promise => { +export const replaceSetByIds = async (sqon: SetSqon, accessToken: string): Promise => { if (!sqon) { throw new Error('Sqon is missing'); } @@ -26,7 +26,7 @@ export const replaceSetByIds = async (sqon: SetSqon, accessToken: string, userId const matchesSet = setRegex.exec(content?.content?.value?.[0]); const setId: string | null = matchesSet && matchesSet[CAPTURING_GROUP_OF_SET_ID_VALUE]; if (setId) { - const set = await getUserSet(accessToken, userId, setId); + const set = await getUserSet(accessToken, setId); const newContent = { ...content }; newContent.content.field = getPathToParticipantId(set.content.setType); newContent.content.value = set.content.ids; diff --git a/src/userApi/userApiClient.test.ts b/src/userApi/userApiClient.test.ts index ea5d49c..599354b 100644 --- a/src/userApi/userApiClient.test.ts +++ b/src/userApi/userApiClient.test.ts @@ -1,31 +1,23 @@ import fetch from 'node-fetch'; -import { CreateUpdateBody, deleteRiff, getRiffs, postRiff, putRiff, Output, Content } from '../riff/riffClient'; +import { getUserContents } from './userApiClient'; import { UserApiError } from './userApiError'; -import {getUserContents} from "./userApiClient"; jest.mock('node-fetch'); describe('UserApi Client', () => { const accessToken = 'Bearer bearer'; - const userId = 'user_id'; const setId = '1ea'; - const createUpdatePayload = { - alias: 'tag', - content: {}, - sharedPublicly: false, - } as CreateUpdateBody; - const output = { id: setId, uid: 'abcedfghijkl', - content: {} as Content, + content: {}, alias: 'tag', sharedPublicly: false, creationDate: new Date(), updatedDate: new Date(), - } as Output; + }; describe('Get user Sets', () => { beforeEach(() => { @@ -65,122 +57,4 @@ describe('UserApi Client', () => { } }); }); - - describe('Post userContents', () => { - beforeEach(() => { - ((fetch as unknown) as jest.Mock).mockReset(); - }); - - it('should return body if status is 200', async () => { - const mockResponse = { status: 200, json: () => output }; - ((fetch as unknown) as jest.Mock).mockImplementation(() => mockResponse); - - const result = await postRiff(accessToken, createUpdatePayload); - - expect(result).toEqual(output); - expect(((fetch as unknown) as jest.Mock).mock.calls.length).toEqual(1); - }); - - it('should throw a UserApiError if status is not 200', async () => { - const expectedBadRequest = { - timestamp: '2021-09-24T15:08:44.482+00:00', - status: 400, - error: 'Bad Request', - message: '', - path: '/riff/shorten', - }; - - const expectedError = new UserApiError(400, expectedBadRequest); - const mockResponse = { status: 400, json: () => expectedBadRequest }; - - ((fetch as unknown) as jest.Mock).mockImplementation(() => mockResponse); - - try { - await postRiff(accessToken, createUpdatePayload); - } catch (e) { - expect(e).toEqual(expectedError); - } finally { - expect(((fetch as unknown) as jest.Mock).mock.calls.length).toEqual(1); - } - }); - }); - - describe('Put User Content', () => { - beforeEach(() => { - ((fetch as unknown) as jest.Mock).mockReset(); - }); - - it('should return body if status is 200', async () => { - const updateRiff = { ...output, alias: 'tag updated', updatedDate: new Date() }; - const mockResponse = { status: 200, json: () => updateRiff }; - ((fetch as unknown) as jest.Mock).mockImplementation(() => mockResponse); - - const result = await putRiff(accessToken, { ...createUpdatePayload, alias: 'tag updated' }, setId); - - expect(result).toEqual(updateRiff); - expect(((fetch as unknown) as jest.Mock).mock.calls.length).toEqual(1); - }); - - it('should throw a UserApiError if status is not 200', async () => { - const expectedNotFound = { - timestamp: '2021-09-24T15:41:35.842+00:00', - status: 404, - error: 'Not Found', - message: '', - path: '/riff/1ea', - }; - - const expectedError = new UserApiError(404, expectedNotFound); - const mockResponse = { status: 404, json: () => expectedNotFound }; - - ((fetch as unknown) as jest.Mock).mockImplementation(() => mockResponse); - - try { - await putRiff(accessToken, { ...createUpdatePayload, alias: 'tag updated' }, setId); - } catch (e) { - expect(e).toEqual(expectedError); - } finally { - expect(((fetch as unknown) as jest.Mock).mock.calls.length).toEqual(1); - } - }); - }); - - describe('Delete User Content', () => { - beforeEach(() => { - ((fetch as unknown) as jest.Mock).mockReset(); - }); - - it('should return body if status is 200', async () => { - const mockResponse = { status: 200, json: () => true }; - ((fetch as unknown) as jest.Mock).mockImplementation(() => mockResponse); - - const result = await deleteRiff(accessToken, setId); - - expect(result).toEqual(true); - expect(((fetch as unknown) as jest.Mock).mock.calls.length).toEqual(1); - }); - - it('should throw a RiffError if status is not 200', async () => { - const expectedUnauthorized = { - timestamp: '2021-09-24T15:12:06.959+00:00', - status: 401, - error: 'Unauthorized', - message: '', - path: '/riff/1ea', - }; - - const expectedError = new UserApiError(401, expectedUnauthorized); - const mockResponse = { status: 401, json: () => expectedUnauthorized }; - - ((fetch as unknown) as jest.Mock).mockImplementation(() => mockResponse); - - try { - await deleteRiff(accessToken, setId); - } catch (e) { - expect(e).toEqual(expectedError); - } finally { - expect(((fetch as unknown) as jest.Mock).mock.calls.length).toEqual(1); - } - }); - }); }); diff --git a/src/userApi/userApiClient.ts b/src/userApi/userApiClient.ts index e3c47d3..0749509 100644 --- a/src/userApi/userApiClient.ts +++ b/src/userApi/userApiClient.ts @@ -2,12 +2,10 @@ import fetch from 'node-fetch'; import { SetSqon, Sort } from '../endpoints/sets/setsTypes'; import { userApiURL } from '../env'; -import { CreateUpdateBody } from '../riff/riffClient'; import { UserApiError } from './userApiError'; export type Content = { setType: string; - riffType: string; ids: string[]; sqon: SetSqon; sort: Sort[]; @@ -64,7 +62,7 @@ export const getUserContents = async (accessToken: string): Promise => throw new UserApiError(response.status, body); }; -export const postUserContent = async (accessToken: string, set: CreateUpdateBody): Promise => { +export const postUserContent = async (accessToken: string, set): Promise => { const uri = `${userApiURL}/user-sets`; const response = await fetch(encodeURI(uri), { @@ -85,7 +83,7 @@ export const postUserContent = async (accessToken: string, set: CreateUpdateBody throw new UserApiError(response.status, body); }; -export const putUserContent = async (accessToken: string, set: CreateUpdateBody, setId: string): Promise => { +export const putUserContent = async (accessToken: string, set, setId: string): Promise => { const uri = `${userApiURL}/user-sets/${setId}`; const response = await fetch(encodeURI(uri), { diff --git a/src/userApi/userApiError.ts b/src/userApi/userApiError.ts index 1c50e55..b10e00c 100644 --- a/src/userApi/userApiError.ts +++ b/src/userApi/userApiError.ts @@ -3,7 +3,7 @@ export class UserApiError extends Error { public readonly details: unknown; constructor(status: number, details: unknown) { - super(`Riff returns status ${status}`); + super(`UserApi returns status ${status}`); Object.setPrototypeOf(this, UserApiError.prototype); this.name = UserApiError.name; this.status = status;