🔥 Remove code related to portal-legacy

kids-first · Jun 27, 2024 · b8a8a8d · b8a8a8d
1 parent 9d08981
commit b8a8a8d
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Showing 34 changed files with 2,302 additions and 7,271 deletions.
diff --git 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
diff --git 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
@@ -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
diff --git a/src/SQS/sendEvent.ts b/src/SQS/sendEvent.ts
diff --git a/src/app.test.ts b/src/app.test.ts
@@ -1,12 +1,10 @@
-import { SQSClient } from '@aws-sdk/client-sqs';
 import { Express } from 'express';
 import Keycloak from 'keycloak-connect';
 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
@@ -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 });
@@ -88,26 +85,17 @@ 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);
     });
 
     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
@@ -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);