port tests to mocha to avoid bug with jest and File

Signed-off-by: Steve Cassidy <[email protected]>

.mocharc.json

@@ -0,0 +1,8 @@
+{
+    "extension": ["ts"],
+    "spec": "test/*.test.ts",
+    "require": [
+        "ts-node/register"
+    ],
+    "recursive": true
+}

package.json

@@ -11,11 +11,11 @@
     "prestart": "npm run-script compile",
     "start": "node .",
     "watch": "nodemon --ignore build --ext ts --exec 'tsc --incremental && node .'",
-    "test": "env-cmd jest --silent=false test/*.test.ts",
-    "test:watch": "env-cmd jest --watch",
-    "coverage": "env-cmd jest --coverage test/*.test.ts",
     "initdb": "env-cmd node scripts/initialise.js",
-    "load-notebooks": "env-cmd node scripts/loadNotebook.js ./notebooks/*.json"
+    "load-notebooks": "env-cmd node scripts/loadNotebook.js ./notebooks/*.json",
+    "test": "env-cmd cross-env NODE_ENV=test TS_NODE_PROJECT='./tsconfig.json' mocha",
+    "test:watch": "env-cmd cross-env NODE_ENV=test TS_NODE_PROJECT='./tsconfig.json' mocha -w",
+    "coverage": "nyc env-cmd cross-env NODE_ENV=test TS_NODE_PROJECT='./tsconfig.json' mocha"
   },
   "dependencies": {
     "archiver": "^6.0.1",
@@ -31,10 +31,12 @@
     "fast-check": "2.25.0",
     "gts": "3.1.1",
     "handlebars": "4.7.7.",
+    "istanbul": "^0.4.5",
     "jose": "4.15.2",
     "morgan": "^1.10.0",
     "multer": "^1.4.5-lts.1",
     "nodemailer": "^6.9.5",
+    "nyc": "^15.1.0",
     "oauth": "0.10.0",
     "passport": "0.5.3",
     "passport-google-oauth20": "2.0.0",
@@ -45,21 +47,19 @@
     "pouchdb-security-helper": "^2.1.2",
     "qrcode": "^1.5.3",
     "req-flash": "^0.0.3",
-    "supertest": "6.3.3",
     "swagger-ui-dist": "^5.1.0",
-    "ts-jest": "27.1.4",
-    "ts-node": "10.9.1",
     "typescript": "4.9.5",
     "uuid": "9.0.1"
   },
   "devDependencies": {
     "@types/archiver": "^5.3.4",
+    "@types/chai": "^4.3.9",
     "@types/cookie-session": "2.0.45",
     "@types/cors": "2.8.13",
     "@types/express": "4.17.18",
     "@types/express-handlebars": "5.3.1",
     "@types/express-session": "1.17.5",
-    "@types/jest": "27.5.0",
+    "@types/mocha": "^10.0.3",
     "@types/morgan": "^1.9.5",
     "@types/multer": "^1.4.7",
     "@types/node": "18.14.2",
@@ -70,17 +70,22 @@
     "@types/passport-oauth2": "1.4.13",
     "@types/pouchdb": "6.4.0",
     "@types/qrcode": "^1.5.2",
+    "@types/sinon": "^10.0.20",
     "@types/supertest": "2.0.12",
     "@types/swagger-ui-dist": "^3.30.1",
     "@types/uuid": "9.0.4",
+    "chai": "^4.3.10",
+    "cross-env": "^7.0.3",
     "dotenv": "^16.3.1",
     "env-cmd": "^10.1.0",
-    "jest": "^27.5.1",
     "jest-fast-check": "1.0.2",
+    "mocha": "^10.2.0",
     "nano": "^10.1.2",
     "node-fetch": "^3.3.2",
     "nodemon": "^2.0.20",
     "pouchdb-adapter-memory": "^8.0.1",
-    "supertest": "^6.3.3"
+    "sinon": "^17.0.0",
+    "supertest": "^6.3.3",
+    "ts-node": "10.9.1"
   }
 }

src/authkeys/read.ts

@@ -29,7 +29,6 @@ import {getSigningKey} from './signing_keys';
  */
 export const validateToken = async (token: string) => {
   const signingKey = await getSigningKey();
-
   //console.log(`verifying token: '${token}'`);
   try {
     const {payload} = await jwtVerify(token, signingKey.public_key, {
@@ -39,7 +38,7 @@ export const validateToken = async (token: string) => {
     //console.log('Token Payload', payload);
 
     if (payload.sub) {
-      const user = getUserFromEmailOrUsername(payload.sub);
+      const user = await getUserFromEmailOrUsername(payload.sub);
       return user;
     } else {
       return undefined;

src/couchdb/backupRestore.ts

@@ -18,8 +18,9 @@
  *    Functions to backup and restore databases
  */
 import {open} from 'node:fs/promises';
-import {getProjectDataDB, getProjectMetaDB, getProjectsDB} from '.';
+import {getProjectsDB} from '.';
 import {addDesignDocsForNotebook} from './notebooks';
+import {getDataDB, getProjectDB} from 'faims3-datamodel';
 
 /**
  * restoreFromBackup - restore databases from a JSONL backup file
@@ -45,10 +46,10 @@ export const restoreFromBackup = async (filename: string) => {
         db = await getProjectsDB();
       } else if (dbName.startsWith('metadata')) {
         const projectName = dbName.split('||')[1];
-        db = await getProjectMetaDB(projectName);
+        db = await getProjectDB(projectName);
       } else if (dbName.startsWith('data')) {
         const projectName = dbName.split('||')[1];
-        db = await getProjectDataDB(projectName);
+        db = await getDataDB(projectName);
         if (db) {
           addDesignDocsForNotebook(db);
           // TODO: set up permissions for the databases
@@ -68,7 +69,7 @@ export const restoreFromBackup = async (filename: string) => {
       try {
         await db.put(doc.doc);
       } catch (error) {
-        console.log('Error restoring document', doc.id, error);
+        console.log('Error restoring document', doc.id)//, error);
       }
     }
   }

src/couchdb/index.ts

@@ -81,6 +81,7 @@ export const getPublicUserDbURL = (): string => {
 export const getUsersDB = (): PouchDB.Database | undefined => {
   if (!_usersDB) {
     const pouch_options = pouchOptions();
+
     const dbName = COUCHDB_INTERNAL_URL + PEOPLE_DB_NAME;
     _usersDB = new PouchDB(dbName, pouch_options);
   }

src/couchdb/initialise.ts

@@ -129,7 +129,6 @@ export const initialiseUserDB = async (db: PouchDB.Database | undefined) => {
       security.members.roles.removeAll();
       await security.save();
     }
-
     const [user, error] = await registerLocalUser(
       'admin',
       '', // no email address

src/couchdb/notebooks.ts

@@ -73,6 +73,7 @@ export const getNotebooks = async (user: Express.User): Promise<any[]> => {
         projects.push(e.doc as unknown as ProjectObject);
       }
     });
+
     for (const project of projects) {
       const project_id = project._id;
       const full_project_id = resolve_project_id(listing_id, project_id);
@@ -548,15 +549,14 @@ export const notebookRecordIterator = async (
 ) => {
   let records = await getRecordsWithRegex(project_id, '.*', true);
   let index = 0;
-
   // select just those in this view
   records = records.filter((record: any) => {
     return record.type === viewid;
   });
 
   const recordIterator = {
     async next() {
-      if (index < records.length - 1) {
+      if (index < records.length) {
         const data = await getFullRecordData(
           project_id,
           records[index].record_id,

src/couchdb/users.ts

@@ -179,7 +179,9 @@ async function getUserFromUsername(
   const users_db = getUsersDB();
   if (users_db) {
     try {
-      return (await users_db.get(username)) as Express.User;
+      const user = (await users_db.get(username)) as Express.User;
+      return user;
+      //return (await users_db.get(username)) as Express.User;
     } catch (err) {
       return null;
     }

src/index.ts

@@ -30,11 +30,11 @@ import {registerClient} from 'faims3-datamodel';
 import {getProjectDataDB, getProjectMetaDB} from './couchdb';
 
 // set up the database module faims3-datamodel with our callbacks to get databases
-registerClient({
-  getDataDB: getProjectDataDB,
-  getProjectDB: getProjectMetaDB,
-  shouldDisplayRecord: () => true,
-});
+// registerClient({
+//   getDataDB: getProjectDataDB,
+//   getProjectDB: getProjectMetaDB,
+//   shouldDisplayRecord: () => true,
+// });
 
 process.on('unhandledRejection', error => {
   console.error('unhandledRejection');

test/api.test.ts

@@ -26,8 +26,8 @@ import request from 'supertest';
 import {app} from '../src/routes';
 import {initialiseDatabases} from '../src/couchdb';
 import {
-  createUser,
   getUserFromEmailOrUsername,
+  createUser,
   saveUser,
 } from '../src/couchdb/users';
 import {createAuthKey} from '../src/authkeys/create';
@@ -36,6 +36,7 @@ import fs from 'fs';
 import {createNotebook} from '../src/couchdb/notebooks';
 import {ProjectUIModel} from 'faims3-datamodel';
 import {DEVELOPER_MODE} from '../src/buildconfig';
+import {expect} from 'chai';
 
 const uispec: ProjectUIModel = {
   fields: [],
@@ -47,45 +48,43 @@ const uispec: ProjectUIModel = {
 let adminToken = '';
 const username = 'bobalooba';
 
-beforeAll(async () => {
+before(async () => {
   await initialiseDatabases();
   const signing_key = await getSigningKey();
   const adminUser = await getUserFromEmailOrUsername('admin');
   if (adminUser) {
     adminToken = await createAuthKey(adminUser, signing_key);
-
-    const [user, error] = await createUser('', username);
+    const [user, _error] = await createUser('', username);
     if (user) {
       await saveUser(user);
-    } else {
-      throw new Error(error);
     }
   }
 });
 
-test('check is up - not authenticated', async () => {
+it('check is up - not authenticated', async () => {
   const result = await request(app).get('/api/hello');
-  expect(result.statusCode).toBe(401);
+  expect(result.statusCode).to.equal(401);
 });
 
-test('check is up - authenticated', async () => {
+it('check is up - authenticated', async () => {
+  console.log('check is up - authenticated');
   const result = await request(app)
     .get('/api/hello')
     .set('Authorization', `Bearer ${adminToken}`);
-  expect(result.statusCode).toBe(200);
+  expect(result.statusCode).to.equal(200);
 });
 
-test('get notebooks', () => {
+it('get notebooks', () => {
   return request(app)
     .get('/api/notebooks')
     .set('Authorization', `Bearer ${adminToken}`)
     .expect(200)
     .expect(response => {
-      expect(response.body).toEqual([]);
+      expect(response.body).to.be.empty;
     });
 });
 
-test('create notebook', () => {
+it('create notebook', () => {
   const filename = 'notebooks/sample_notebook.json';
   const jsonText = fs.readFileSync(filename, 'utf-8');
   const {metadata, 'ui-specification': uiSpec} = JSON.parse(jsonText);
@@ -101,11 +100,11 @@ test('create notebook', () => {
     .set('Content-Type', 'application/json')
     .expect(200)
     .expect(response => {
-      expect(response.body.notebook).toMatch('-test-notebook');
+      expect(response.body.notebook).to.include('-test-notebook');
     });
 });
 
-test('update notebook', () => {
+it('update notebook', () => {
   const filename = 'notebooks/sample_notebook.json';
   const jsonText = fs.readFileSync(filename, 'utf-8');
   const {metadata, 'ui-specification': uiSpec} = JSON.parse(jsonText);
@@ -172,12 +171,12 @@ test('update notebook', () => {
         .set('Content-Type', 'application/json')
         .expect(200)
         .expect(response => {
-          expect(response.body.notebook).toMatch('-test-notebook');
+          expect(response.body.notebook).to.include('-test-notebook');
         });
     });
 });
 
-test('get notebook', async () => {
+it('get notebook', async () => {
   const filename = 'notebooks/sample_notebook.json';
   const jsonText = fs.readFileSync(filename, 'utf-8');
   const {metadata, 'ui-specification': uiSpec} = JSON.parse(jsonText);
@@ -191,23 +190,23 @@ test('get notebook', async () => {
       .set('Content-Type', 'application/json')
       .expect(200)
       .expect(response => {
-        expect(response.body.metadata.name).toEqual('test-notebook');
+        expect(response.body.metadata.name).to.equal('test-notebook');
       });
   } else {
     fail('unable to create test notebook');
   }
 });
 
-test('update admin user - no auth', async () => {
-  return request(app)
+it('update admin user - no auth', async () => {
+  return await request(app)
     .post(`/api/users/${username}/admin`)
     .send({addrole: true})
     .set('Content-Type', 'application/json')
     .expect(401);
 });
 
-test('update admin user - add role', () => {
-  return request(app)
+it('update admin user - add role', async () => {
+  return await request(app)
     .post(`/api/users/${username}/admin`)
     .set('Authorization', `Bearer ${adminToken}`)
     .set('Content-Type', 'application/json')
@@ -216,7 +215,7 @@ test('update admin user - add role', () => {
     .expect({status: 'success'});
 });
 
-test('update admin user - remove role', () => {
+it('update admin user - remove role', () => {
   return request(app)
     .post(`/api/users/${username}/admin`)
     .set('Authorization', `Bearer ${adminToken}`)
@@ -226,7 +225,7 @@ test('update admin user - remove role', () => {
     .expect({status: 'success'});
 });
 
-test('get notebook users', async () => {
+it('get notebook users', async () => {
   const filename = 'notebooks/sample_notebook.json';
   const jsonText = fs.readFileSync(filename, 'utf-8');
   const {metadata, 'ui-specification': uiSpec} = JSON.parse(jsonText);
@@ -239,17 +238,17 @@ test('get notebook users', async () => {
     .set('Content-Type', 'application/json')
     .expect(200)
     .then(response => {
-      expect(response.body.roles).toEqual([
+      expect(response.body.roles).to.deep.equal([
         'admin',
         'moderator',
         'team',
         'user',
       ]);
-      expect(response.body.users.length).toEqual(1);
+      expect(response.body.users.length).to.equal(1);
     });
 });
 
-test('update notebook roles', async () => {
+it('update notebook roles', async () => {
   // make some notebooks
   const nb1 = await createNotebook('NB1', uispec, {});
 
@@ -271,7 +270,7 @@ test('update notebook roles', async () => {
 });
 
 if (DEVELOPER_MODE) {
-  test('create random record', async () => {
+  it('create random record', async () => {
     const nb1 = await createNotebook('NB1', uispec, {});
 
     if (nb1) {