@openneuro/server 4.12.6 → 4.13.0-alpha.0

package/Dockerfile

@@ -4,7 +4,7 @@ FROM openneuro/node AS build
 WORKDIR /srv/packages/openneuro-server
 RUN yarn build
 
-FROM node:14.16.0-alpine3.12
+FROM node:18.12.0-alpine
 
 WORKDIR /srv
 

package/package.json

@@ -1,14 +1,13 @@
 {
   "name": "@openneuro/server",
-  "version": "4.12.6",
+  "version": "4.13.0-alpha.0",
   "description": "Core service for the OpenNeuro platform.",
   "license": "MIT",
   "main": "src/server.js",
   "scripts": {
     "lint": "eslint src",
     "build": "tsc -b",
-    "start": "nodemon --watch ./dist --enable-source-maps ./dist/server.js",
-    "test": "yarn jest"
+    "start": "nodemon --watch ./dist --enable-source-maps ./dist/server.js"
   },
   "repository": {
     "type": "git",
@@ -18,7 +17,7 @@
   "dependencies": {
     "@apollo/client": "3.4.17",
     "@elastic/elasticsearch": "7.15.0",
-    "@openneuro/search": "^4.12.6",
+    "@openneuro/search": "^4.13.0-alpha.0",
     "@passport-next/passport-google-oauth2": "^1.0.0",
     "@sentry/node": "^4.5.3",
     "apollo-server": "2.25.4",
@@ -43,14 +42,12 @@
     "graphql-tools": "4.0.6",
     "immutable": "^3.8.2",
     "ioredis": "4.17.3",
-    "jest-fetch-mock": "^3.0.3",
     "jsdom": "^11.6.2",
     "jsonwebtoken": "^8.3.0",
     "mime-types": "^2.1.19",
     "moment": "^2.14.1",
     "mongoose": "^6.2.3",
     "morgan": "^1.6.1",
-    "node-fetch": "^2.6.0",
     "node-mailjet": "^3.3.5",
     "object-hash": "2.1.1",
     "passport": "^0.6.0",
@@ -82,28 +79,21 @@
     "@babel/runtime-corejs3": "^7.13.10",
     "@types/draft-js": "^0.10.43",
     "@types/ioredis": "^4.17.1",
-    "@types/jest": "^26.0.23",
     "@types/node-mailjet": "^3",
     "@types/semver": "^5",
     "apollo-link-schema": "^1.2.5",
     "babel-eslint": "^10.1.0",
     "core-js": "^3.10.1",
-    "ioredis-mock": "^3.8.1",
-    "jest": "27.5.1",
-    "mockingoose": "2.11.0",
+    "ioredis-mock": "^8.2.2",
     "nodemon": "^2.0.7",
     "supertest": "^3.0.0",
     "ts-node-dev": "1.1.6",
-    "tsc-watch": "^4.2.9"
-  },
-  "jest": {
-    "testEnvironment": "node",
-    "testPathIgnorePatterns": [
-      "dist"
-    ]
+    "tsc-watch": "^4.2.9",
+    "vitest": "^0.25.2",
+    "vitest-fetch-mock": "^0.2.1"
   },
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "fd4d356ca0e88b7a061e0c1feceb07968feed50d"
+  "gitHead": "fe4c230250d73e24a758a0bce058b23aa93d0aee"
 }

package/src/__mocks__/config.js

@@ -1,9 +1,25 @@
-const config = jest.genMockFromModule('../config.js').default
-
-config.auth.jwt.secret = '123456'
-config.datalad.uri = 'datalad'
-config.datalad.workers = 4
-config.mongo.url = 'mongodb://'
-config.notifications.email.from = 'notifications@example.com'
+const config = {
+  auth: {
+    jwt: {
+      secret: '123456',
+    },
+  },
+  datalad: {
+    uri: 'datalad',
+    workers: 4,
+  },
+  mongo: {
+    url: 'mongodb://',
+  },
+  notifications: {
+    email: {
+      from: 'notifications@example.com',
+    },
+  },
+  elasticsearch: {},
+  doi: {
+    username: '',
+  },
+}
 
 export default config

package/src/datalad/__tests__/changelog.spec.js

@@ -1,6 +1,7 @@
 import * as changelog from '../changelog.js'
 
-jest.mock('../../config.js')
+vi.mock('ioredis')
+vi.mock('../../config.js')
 
 describe('changelog editing tools', () => {
   describe('findVersion()', () => {

package/src/datalad/__tests__/dataset.spec.js

@@ -1,26 +1,25 @@
-import mockingoose from 'mockingoose'
+import { vi } from 'vitest'
 import request from 'superagent'
 import { createDataset, datasetsFilter, testBlacklist } from '../dataset.js'
 import { getDatasetWorker } from '../../libs/datalad-service'
+import { connect } from 'mongoose'
 
 // Mock requests to Datalad service
-jest.mock('superagent')
-jest.mock('../../libs/redis.js')
-jest.mock('../../config.js')
-jest.mock('../../libs/notifications.js')
+vi.mock('superagent')
+vi.mock('ioredis')
+vi.mock('../../libs/redis.js')
+vi.mock('../../config.js')
+vi.mock('../../libs/notifications.js')
 
 describe('dataset model operations', () => {
   describe('createDataset()', () => {
-    beforeEach(() => {
-      mockingoose.resetAll()
-      // Setup a default sequence value to return for each test
-      mockingoose.Counter.toReturn(
-        { _id: 'dataset', sequence_value: 1 },
-        'findOne',
-      )
+    beforeAll(() => {
+      // Setup MongoDB with mongodb-memory-server
+      connect(globalThis.__MONGO_URI__)
     })
     it('resolves to dataset id string', async () => {
-      const { id: dsId } = await createDataset(null, null, {
+      const user = { id: '1234' }
+      const { id: dsId } = await createDataset(user.id, user, {
         affirmedDefaced: true,
         affirmedConsent: true,
       })
@@ -28,9 +27,10 @@ describe('dataset model operations', () => {
       expect(dsId.slice(0, 2)).toBe('ds')
     })
     it('posts to the DataLad /datasets/{dsId} endpoint', async () => {
+      const user = { id: '1234' }
       // Reset call count for request.post
       request.post.mockClear()
-      const { id: dsId } = await createDataset(null, null, {
+      const { id: dsId } = await createDataset(user.id, user, {
         affirmedDefaced: true,
         affirmedConsent: true,
       })

package/src/datalad/__tests__/description.spec.js

@@ -7,8 +7,9 @@ import {
 } from '../description.js'
 
 // Mock requests to Datalad service
-jest.mock('superagent')
-jest.mock('../../config.js')
+vi.mock('superagent')
+vi.mock('ioredis')
+vi.mock('../../config.js')
 
 describe('datalad dataset descriptions', () => {
   describe('appendSeniorAuthor', () => {
@@ -89,37 +90,31 @@ describe('datalad dataset descriptions', () => {
       expect(Array.isArray(repaired.Funding)).toBe(true)
     })
   })
-  it('returns the parsed dataset_description.json object', end => {
+  it('returns the parsed dataset_description.json object', async () => {
     request.post.mockClear()
     request.__setMockResponse({
       body: { Name: 'Balloon Analog Risk-taking Task' },
       type: 'application/json',
     })
-    getDescriptionObject('ds000001')([
+    const description = await getDescriptionObject('ds000001')([
       { filename: 'dataset_description.json', id: '12345' },
-    ]).then(description => {
-      expect(description).toEqual({ Name: 'Balloon Analog Risk-taking Task' })
-      end()
-    })
+    ])
+    expect(description).toEqual({ Name: 'Balloon Analog Risk-taking Task' })
   })
-  it('handles a corrupted response', end => {
+  it('handles a corrupted response', async () => {
     request.post.mockClear()
     request.__setMockResponse({
       body: Buffer.from('0x5f3759df', 'hex'),
     })
-    getDescriptionObject('ds000001')([
+    const description = await getDescriptionObject('ds000001')([
       { filename: 'dataset_description.json', id: '12345' },
-    ]).then(description => {
-      expect(description).toEqual(defaultDescription)
-      end()
-    })
+    ])
+    expect(description).toEqual(defaultDescription)
   })
-  it('works without a dataset_description.json being present', end => {
-    getDescriptionObject('ds000001')([
+  it('works without a dataset_description.json being present', async () => {
+    const description = await getDescriptionObject('ds000001')([
       { filename: 'LICENSE', id: '12345' },
-    ]).then(description => {
-      expect(description).toEqual(defaultDescription)
-      end()
-    })
+    ])
+    expect(description).toEqual(defaultDescription)
   })
 })

package/src/datalad/__tests__/files.spec.js

@@ -6,7 +6,8 @@ import {
   computeTotalSize,
 } from '../files.js'
 
-jest.mock('../../config.js')
+vi.mock('ioredis')
+vi.mock('../../config.js')
 
 const filename = 'sub-01/anat/sub-01_T1w.nii.gz'
 
@@ -106,15 +107,17 @@ describe('datalad files', () => {
     })
   })
   describe('computeTotalSize()', () => {
-    const mockFileSizes = [
-      { filename: 'README', size: 234 },
-      { filename: 'dataset_description.json', size: 432 },
-      { filename: 'sub-01/anat/sub-01_T1w.nii.gz', size: 10858 },
-      {
-        filename: 'sub-01/func/sub-01_task-onebacktask_run-01_bold.nii.gz',
-        size: 1945682,
-      },
-    ]
-    expect(computeTotalSize(mockFileSizes)).toBe(1957206)
+    it('computes the size correctly', () => {
+      const mockFileSizes = [
+        { filename: 'README', size: 234 },
+        { filename: 'dataset_description.json', size: 432 },
+        { filename: 'sub-01/anat/sub-01_T1w.nii.gz', size: 10858 },
+        {
+          filename: 'sub-01/func/sub-01_task-onebacktask_run-01_bold.nii.gz',
+          size: 1945682,
+        },
+      ]
+      expect(computeTotalSize(mockFileSizes)).toBe(1957206)
+    })
   })
 })

package/src/datalad/__tests__/pagination.spec.js

@@ -1,6 +1,8 @@
-import mockingoose from 'mockingoose'
+import { vi } from 'vitest'
+vi.mock('ioredis')
 import * as pagination from '../pagination.js'
-import { Types } from 'mongoose'
+import { connect, Types } from 'mongoose'
+import Dataset from '../../models/dataset'
 const ObjectID = Types.ObjectId
 
 const base64 = /^([A-Za-z0-9+/]{4})*([A-Za-z0-9+/]{3}=|[A-Za-z0-9+/]{2}==)?$/
@@ -35,31 +37,23 @@ describe('pagination model operations', () => {
     })
   })
   describe('datasetsConnection()', () => {
-    beforeEach(() => {
-      mockingoose.resetAll()
-      mockingoose.Dataset.toReturn(
-        [
-          {
-            datasets: [
-              {
-                _id: ObjectID('5bef51a1ed211400c08e5524'),
-                id: 'ds001001',
-                created: new Date('2018-11-16T23:24:17.203Z'),
-                modified: new Date('2018-11-16T23:24:25.050Z'),
-                uploader: 'f8d5a57c-879a-40e6-b151-e34c4a28ff70',
-                revision: '262a8e610e32b5766cbf669acc71911c1ece7126',
-              },
-            ],
-            count: 1,
-          },
-        ],
-        'aggregate',
-      )
+    beforeAll(async () => {
+      await connect(globalThis.__MONGO_URI__)
+      const ds = new Dataset({
+        _id: ObjectID('5bef51a1ed211400c08e5524'),
+        id: 'ds001001',
+        created: new Date('2018-11-16T23:24:17.203Z'),
+        modified: new Date('2018-11-16T23:24:25.050Z'),
+        uploader: 'f8d5a57c-879a-40e6-b151-e34c4a28ff70',
+        revision: '262a8e610e32b5766cbf669acc71911c1ece7126',
+      })
+      await ds.save()
     })
     it('returns a connection shaped result', async () => {
       const res = await pagination.datasetsConnection({
         orderBy: { created: 'ascending' },
         limit: 5,
+        first: 10,
       })([])
       expect(res).toHaveProperty('pageInfo')
       expect(res).toHaveProperty('edges')

package/src/datalad/__tests__/snapshots.spec.js

@@ -1,39 +1,35 @@
-import mockingoose from 'mockingoose'
+import { vi } from 'vitest'
+vi.mock('ioredis')
 import request from 'superagent'
 import { createDataset } from '../dataset.js'
 import { createSnapshot } from '../snapshots.js'
 import { getDatasetWorker } from '../../libs/datalad-service'
+import { connect } from 'mongoose'
 
 // Mock requests to Datalad service
-jest.mock('superagent')
-jest.mock('../../libs/redis.js', () => ({
+vi.mock('superagent')
+vi.mock('../../libs/redis.js', () => ({
   redis: {
-    del: jest.fn(),
+    del: vi.fn(),
   },
   redlock: {
-    lock: jest.fn().mockImplementation(() => ({ unlock: jest.fn() })),
+    lock: vi.fn().mockImplementation(() => ({ unlock: vi.fn() })),
   },
 }))
 // Mock draft files calls
-jest.mock('../draft.js', () => ({
+vi.mock('../draft.js', () => ({
   updateDatasetRevision: () => () => Promise.resolve(),
 }))
-jest.mock('../../config.js')
-jest.mock('../../libs/notifications.js')
+vi.mock('../../config.js')
+vi.mock('../../libs/notifications.js')
 
 describe('snapshot model operations', () => {
   describe('createSnapshot()', () => {
-    beforeEach(() => {
-      mockingoose.resetAll()
-      // Setup a default sequence value to return for each test
-      mockingoose.Counter.toReturn(
-        { _id: 'dataset', sequence_value: 1 },
-        'findOne',
-      )
-    })
     it('posts to the DataLad /datasets/{dsId}/snapshots/{snapshot} endpoint', async () => {
+      const user = { id: '1234' }
       const tag = 'snapshot'
-      const { id: dsId } = await createDataset(null, null, {
+      await connect(globalThis.__MONGO_URI__)
+      const { id: dsId } = await createDataset(user.id, user, {
         affirmedDefaced: true,
         affirmedConsent: true,
       })

package/src/datalad/changelog.js

@@ -1,4 +1,3 @@
-import fetch from 'node-fetch'
 import format from 'date-fns/format'
 import { addFileString, commitFiles } from './dataset.js'
 import { getDatasetWorker } from '../libs/datalad-service'

package/src/datalad/draft.js

@@ -1,7 +1,6 @@
 /**
  * Manage serving a Draft object based on DataLad working trees
  */
-import fetch from 'node-fetch'
 import request from 'superagent'
 import Dataset from '../models/dataset'
 import publishDraftUpdate from '../graphql/utils/publish-draft-update.js'

package/src/datalad/readme.js

@@ -1,4 +1,3 @@
-import fetch from 'node-fetch'
 import { addFileString, commitFiles } from './dataset'
 import { redis } from '../libs/redis'
 import CacheItem, { CacheType } from '../cache/item'

package/src/datalad/upload.js

@@ -1,4 +1,3 @@
-import fetch from 'node-fetch'
 import { getDatasetWorker } from '../libs/datalad-service'
 
 export const uploadUrl = (datasetId, uploadId) => {

package/src/elasticsearch/reindex-dataset.ts

@@ -1,3 +1,4 @@
+import config from '../config.js'
 import { indexDataset, queryForIndex, indexingToken } from '@openneuro/search'
 import { elasticClient } from './elastic-client'
 import {
@@ -8,13 +9,12 @@ import {
 } from '@apollo/client'
 import { setContext } from '@apollo/client/link/context'
 import { HttpLink } from '@apollo/client/link/http'
-import fetch from 'node-fetch'
 
 /**
  * Setup SchemaLink based client for querying
  */
 export const schemaLinkClient = (): ApolloClient<NormalizedCacheObject> => {
-  const accessToken = indexingToken()
+  const accessToken = indexingToken(config.auth.jwt.secret)
   const authLink = setContext((_, { headers }) => {
     return {
       headers: {
@@ -25,7 +25,6 @@ export const schemaLinkClient = (): ApolloClient<NormalizedCacheObject> => {
   })
   const httpLink = new HttpLink({
     uri: process.env.GRAPHQL_URI,
-    fetch,
   })
   return new ApolloClient({
     link: from([authLink, httpLink]),

package/src/graphql/__tests__/__snapshots__/permissions.spec.js.snap

@@ -1,5 +1,5 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
+// Vitest Snapshot v1
 
-exports[`resolver permissions helpers checkDatasetAdmin() resolves to false for anonymous users 1`] = `"You do not have admin access to this dataset."`;
+exports[`resolver permissions helpers > checkDatasetAdmin() > resolves to false for anonymous users 1`] = `"You do not have admin access to this dataset."`;
 
-exports[`resolver permissions helpers checkDatasetWrite() resolves to false for anonymous users 1`] = `"You do not have access to modify this dataset."`;
+exports[`resolver permissions helpers > checkDatasetWrite() > resolves to false for anonymous users 1`] = `"You do not have access to modify this dataset."`;

package/src/graphql/__tests__/comment.spec.js

@@ -1,50 +1,37 @@
-import mockingoose from 'mockingoose'
+import { vi } from 'vitest'
+import { connect } from 'mongoose'
 import { deleteComment, flatten } from '../resolvers/comment'
 import Comment from '../../models/comment'
 
-const incrementHex = hex => {
-  hex = hex.toString()
-  const splitLen = 14
-  const start = hex.substr(0, splitLen)
-  const end = hex.substr(splitLen)
-  let dec = parseInt(end, 16)
-  dec++
-  return start + dec.toString(16)
-}
+vi.mock('ioredis')
 
 describe('comment resolver helpers', () => {
   describe('deleteComment', () => {
     let aId
-    let commentA
-    let adminUser, nonAdminUser
-    beforeEach(async () => {
-      mockingoose.resetAll()
-      adminUser = {
-        user: 'userid',
-        userInfo: { admin: true },
-      }
-      nonAdminUser = {
-        user: 'userid',
-        userInfo: { admin: false },
-      }
-      commentA = {
+    const adminUser = {
+      user: '1234',
+      userInfo: { admin: true },
+    }
+    const nonAdminUser = {
+      user: '5678',
+      userInfo: { admin: false },
+    }
+    beforeAll(async () => {
+      await connect(globalThis.__MONGO_URI__)
+      const comment = new Comment({
         text: 'a',
         createDate: new Date().toISOString(),
-        user: { __typename: 'User', _id: 'userid' },
-      }
-      mockingoose.Comment.toReturn(commentA, 'findOne')
-      aId = (await Comment.findById('just getting commentA here').exec())._id
-      mockingoose.Comment.toReturn([], 'find')
+        user: { id: '5678' },
+      })
+      await comment.save()
+      aId = comment.id
     })
 
     it('returns an array of the deleted comment ids', async () => {
       const deletedIds = (
         await deleteComment({}, { commentId: aId }, adminUser)
       ).map(id => id.toString())
-
-      // mockingoose ids are sequential, and the documents returned from each query get new ids for some reason
-      //   TODO: Replace mockingoose with better library
-      expect(deletedIds[0].slice(-5)).toEqual(incrementHex(aId).slice(-5))
+      expect(deletedIds[0]).toEqual(aId)
     })
 
     it('prevents non-admin users from deleting comments', () => {
@@ -55,11 +42,13 @@ describe('comment resolver helpers', () => {
   })
 
   describe('flatten', () => {
-    const arrarr = [
-      [1, 2, 3],
-      [4, 5],
-    ]
-    const arr = flatten(arrarr)
-    expect(arr).toEqual([1, 2, 3, 4, 5])
+    it('unrolls an array', () => {
+      const arrarr = [
+        [1, 2, 3],
+        [4, 5],
+      ]
+      const arr = flatten(arrarr)
+      expect(arr).toEqual([1, 2, 3, 4, 5])
+    })
   })
 })

package/src/graphql/__tests__/permissions.spec.js

@@ -6,6 +6,8 @@ import {
   checkDatasetAdmin,
 } from '../permissions.js'
 
+vi.mock('ioredis')
+
 describe('resolver permissions helpers', () => {
   describe('datasetReadQuery()', () => {
     it('returns public for anonymous users', () => {

package/src/graphql/resolvers/__tests__/brainlife.spec.ts

@@ -1,6 +1,9 @@
+import { vi } from 'vitest'
 import { HasId } from '../../../utils/datasetOrSnapshot'
 import { brainlifeQuery } from '../brainlife'
 
+vi.mock('ioredis')
+
 describe('brainlife resolvers', () => {
   it('correctly queries drafts', () => {
     expect(brainlifeQuery({ id: 'ds000001' } as HasId).toString()).toEqual(

package/src/graphql/resolvers/__tests__/dataset-search.spec.js

@@ -4,8 +4,9 @@ import {
   elasticRelayConnection,
 } from '../dataset-search'
 
-jest.mock('../../../elasticsearch/elastic-client.js')
-jest.mock('../../../config.js')
+vi.mock('ioredis')
+vi.mock('../../../elasticsearch/elastic-client.js')
+vi.mock('../../../config.js')
 
 describe('dataset search resolvers', () => {
   describe('encodeCursor()', () => {
@@ -46,14 +47,14 @@ describe('dataset search resolvers', () => {
         },
       }
       const connection = await elasticRelayConnection(emptyApiResponse, {
-        dataset: jest.fn(),
+        dataset: vi.fn(),
       })
       expect(connection).toMatchObject(nullRelayConnection)
     })
 
     it('returns a relay cursor for ApiResponse with results', () => {
       const mockResolvers = {
-        dataset: jest.fn(),
+        dataset: vi.fn(),
       }
 
       const expectedApiResponse = {

package/src/graphql/resolvers/__tests__/dataset.spec.js

@@ -1,19 +1,16 @@
-import mockingoose from 'mockingoose'
+import { vi } from 'vitest'
+import { connect } from 'mongoose'
 import request from 'superagent'
 import * as ds from '../dataset'
 
-jest.mock('superagent')
-jest.mock('ioredis')
-jest.mock('../../../config.js')
-jest.mock('../../../libs/notifications.js')
+vi.mock('superagent')
+vi.mock('ioredis')
+vi.mock('../../../config.js')
+vi.mock('../../../libs/notifications.js')
 
 describe('dataset resolvers', () => {
-  beforeEach(() => {
-    mockingoose.resetAll()
-    mockingoose.Counter.toReturn(
-      { _id: 'dataset', sequence_value: 1 },
-      'findOne',
-    )
+  beforeAll(() => {
+    connect(globalThis.__MONGO_URI__)
   })
   describe('createDataset()', () => {
     it('createDataset mutation succeeds', async () => {
@@ -145,12 +142,9 @@ describe('dataset resolvers', () => {
   })
   describe('deleteFiles', () => {
     beforeEach(() => {
-      mockingoose.resetAll()
       request.post.mockClear()
     })
-    it('makes correct delete call to datalad', done => {
-      // pass checkDatasetExists()
-      mockingoose.Dataset.toReturn(true, 'count')
+    it('makes correct delete call to datalad', () => {
       // capture and check datalad delete request
       request.del = url => ({
         set: (header1, headerValue1) => ({
@@ -165,7 +159,7 @@ describe('dataset resolvers', () => {
         }),
       })
 
-      ds.deleteFiles(
+      return ds.deleteFiles(
         null,
         { datasetId: 'ds999999', files: [{ path: '/sub-99' }] },
         {
@@ -175,7 +169,7 @@ describe('dataset resolvers', () => {
             admin: true,
           },
         },
-      ).then(() => done())
+      )
     })
   })
 })

package/src/graphql/resolvers/__tests__/derivatives.spec.ts

@@ -1,5 +1,8 @@
+import { vi } from 'vitest'
 import { githubDerivativeQuery, derivativeObject } from '../derivatives'
 
+vi.mock('ioredis')
+
 describe('GraphQL derivatives', () => {
   describe('githubDerivativeQuery()', () => {
     it('constructs a correct URL', () => {

package/src/graphql/resolvers/__tests__/importRemoteDataset.spec.ts

@@ -1,12 +1,15 @@
-import fetchMock from 'jest-fetch-mock'
+import { vi } from 'vitest'
 import { importRemoteDataset, allowedImportUrl } from '../importRemoteDataset'
-import { checkDatasetWrite } from '../../permissions'
+import createFetchMock from 'vitest-fetch-mock'
 
-jest.mock('../../../config')
-jest.mock('../../permissions')
+vi.mock('ioredis')
+vi.mock('../../../config')
+vi.mock('../../permissions')
 
 describe('importRemoteDataset mutation', () => {
   it('given a user with access, it creates an import record for later processing', () => {
+    const fetchMock = createFetchMock(vi)
+    fetchMock.doMock()
     fetchMock.mockOnce(JSON.stringify(true))
     importRemoteDataset(
       {},

package/src/graphql/resolvers/__tests__/permssions.spec.js

@@ -1,12 +1,13 @@
 import { updatePermissions } from '../permissions'
 
-jest.mock('../../permissions', () => ({
+vi.mock('ioredis')
+vi.mock('../../permissions', () => ({
   checkDatasetAdmin: async () => Promise.resolve(),
 }))
 
-const mockExec = jest.fn()
+const mockExec = vi.fn()
 
-jest.mock('../../../models/user', () => ({
+vi.mock('../../../models/user', () => ({
   find: () => ({
     exec: mockExec,
   }),

package/src/graphql/resolvers/__tests__/snapshots.spec.js

@@ -1,6 +1,8 @@
-jest.mock('../../../config')
 import { matchKnownObjects, filterLatestSnapshot } from '../snapshots.js'
 
+vi.mock('ioredis')
+vi.mock('../../../config.js')
+
 describe('snapshot resolvers', () => {
   describe('matchKnownObjects()', () => {
     it('should return NDA as a source when given a description containing 10.15154 DOIs', () => {

package/src/graphql/resolvers/__tests__/user.spec.js

@@ -1,5 +1,7 @@
 import { users } from '../user.js'
 
+vi.mock('ioredis')
+
 describe('user resolvers', () => {
   describe('users()', () => {
     it('throws an error for non-admins', () => {

package/src/graphql/resolvers/brainlife.ts

@@ -1,4 +1,3 @@
-import fetch from 'node-fetch'
 import {
   DatasetOrSnapshot,
   getDatasetFromSnapshotId,

package/src/graphql/resolvers/dataset-search.js

@@ -1,4 +1,4 @@
-import elasticClient from '../../elasticsearch/elastic-client'
+import { elasticClient } from '../../elasticsearch/elastic-client'
 import { dataset } from './dataset'
 import Star from '../../models/stars'
 import Subscription from '../../models/subscription'
@@ -203,7 +203,15 @@ const parseQuery = async (query, datasetType, datasetStatus, userId) => {
  */
 export const advancedDatasetSearchConnection = async (
   obj,
-  { query, allDatasets = false, datasetType, datasetStatus, sortBy, after, first = 25 },
+  {
+    query,
+    allDatasets = false,
+    datasetType,
+    datasetStatus,
+    sortBy,
+    after,
+    first = 25,
+  },
   { user, userInfo },
 ) => {
   const searchId = hashObject({

package/src/graphql/resolvers/derivatives.ts

@@ -1,4 +1,3 @@
-import fetch from 'node-fetch'
 import {
   DatasetOrSnapshot,
   getDatasetFromSnapshotId,

package/src/graphql/resolvers/history.js

@@ -1,4 +1,3 @@
-import fetch from 'node-fetch'
 import { getDatasetWorker } from '../../libs/datalad-service.js'
 
 export const history = async obj => {

package/src/graphql/resolvers/importRemoteDataset.ts

@@ -1,4 +1,3 @@
-import fetch from 'node-fetch'
 import IngestDataset from '../../models/ingestDataset'
 import { checkDatasetWrite } from '../permissions.js'
 import { getDatasetWorker } from '../../libs/datalad-service'

package/src/graphql/resolvers/validation.js

@@ -1,4 +1,3 @@
-import fetch from 'node-fetch'
 import config from '../../config'
 import { generateDataladCookie } from '../../libs/authentication/jwt'
 import { getDatasetWorker } from '../../libs/datalad-service'

package/src/libs/__tests__/apikey.spec.js

@@ -2,7 +2,8 @@ import jwt from 'jsonwebtoken'
 import { apiKeyFactory } from '../apikey.js'
 import config from '../../config.js'
 
-jest.mock('../../config.js')
+vi.mock('ioredis')
+vi.mock('../../config.js')
 
 const userMock = {
   id: '1337',

package/src/libs/__tests__/datalad-service.spec.js

@@ -1,5 +1,7 @@
 import { hashDatasetToRange } from '../datalad-service'
 
+vi.mock('ioredis')
+
 describe('datalad-service utils', () => {
   describe('hashDatasetToRange()', () => {
     it('is stable across a range of datasets', () => {

package/src/libs/__tests__/dataset.spec.js

@@ -1,39 +1,26 @@
-import mockingoose from 'mockingoose'
+import { vi } from 'vitest'
+import { connect } from 'mongoose'
 import { getAccessionNumber } from '../dataset.js'
 
+vi.mock('ioredis')
+
 describe('libs/dataset.js', () => {
   describe('getAccessionNumber', () => {
-    beforeEach(() => {
-      mockingoose.resetAll()
+    beforeAll(() => {
+      connect(globalThis.__MONGO_URI__)
     })
     it('returns strings starting with "ds"', async () => {
-      mockingoose.Counter.toReturn(
-        { _id: 'dataset', sequence_value: 2 },
-        'findOne',
-      )
       const ds = await getAccessionNumber()
       expect(ds.slice(0, 2)).toEqual('ds')
     })
     it('generates sequential numbers', async () => {
-      mockingoose.Counter.toReturn(
-        { _id: 'dataset', sequence_value: 2 },
-        'findOne',
-      )
       const first = await getAccessionNumber()
-      mockingoose.Counter.toReturn(
-        { _id: 'dataset', sequence_value: 3 },
-        'findOne',
-      )
       const second = await getAccessionNumber()
       const fNum = parseInt(first.slice(2))
       const sNum = parseInt(second.slice(2))
       expect(fNum).toBeLessThan(sNum)
     })
     it('returns 6 digits for ds ids', async () => {
-      mockingoose.Counter.toReturn(
-        { _id: 'dataset', sequence_value: 2 },
-        'findOne',
-      )
       const ds = await getAccessionNumber()
       const num = ds.slice(2)
       expect(num).toHaveLength(6)

package/src/libs/authentication/__tests__/jwt.spec.js

@@ -1,7 +1,9 @@
 import User from '../../../models/user'
 import { addJWT } from '../jwt.js'
 
-jest.mock('../../../config.js')
+vi.mock('ioredis')
+vi.mock('../../../config.js')
+vi.unmock('mongoose')
 
 describe('jwt auth', () => {
   describe('addJWT()', () => {

package/src/libs/counter.js

@@ -5,22 +5,17 @@ import Counter from '../models/counter'
  *
  * A helper library for getting persistent serial numbers.
  */
-export default {
-  /**
-   * Get Next
-   *
-   * Takes any string as a type and callsback with the next
-   * sequential integer for that type starting with 1.
-   */
-  getNext(type, callback) {
-    Counter.findOne({ _id: type }).then(found => {
-      if (found) {
-        Counter.updateOne({ _id: type }, { $inc: { sequence_value: 1 } }).then(
-          callback(found.sequence_value + 1),
-        )
-      } else {
-        Counter.create({ _id: type, sequence_value: 1 }).then(callback(1))
-      }
-    })
-  },
+export async function getNext(type) {
+  const found = await Counter.findOne({ _id: type }).exec()
+  if (found) {
+    await Counter.updateOne(
+      { _id: type },
+      { $inc: { sequence_value: 1 } },
+    ).exec()
+    return found.sequence_value + 1
+  } else {
+    const counter = new Counter({ _id: type, sequence_value: 1 })
+    await counter.save()
+    return 1
+  }
 }

package/src/libs/dataset.js

@@ -1,14 +1,9 @@
-import counter from './counter'
+import { getNext } from './counter'
 
 /**
  * Returns the next accession number string
  */
-export const getAccessionNumber = () => {
-  return new Promise(resolve => {
-    counter.getNext('datasets', datasetNumber => {
-      const offset = 1000
-      datasetNumber += offset
-      resolve('ds' + ('000000' + datasetNumber).substr(-6, 6))
-    })
-  })
+export async function getAccessionNumber() {
+  const datasetNumber = (await getNext('datasets')) + 1000
+  return `ds${('000000' + datasetNumber).substr(-6, 6)}`
 }

package/src/libs/doi/__tests__/__snapshots__/doi.spec.js.snap

@@ -1,6 +1,6 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
+// Vitest Snapshot v1
 
-exports[`DOI minting utils template() accepts expected arguments 1`] = `
+exports[`DOI minting utils > template() > accepts expected arguments 1`] = `
 "<?xml version=\\"1.0\\" encoding=\\"UTF-8\\"?>
 <resource xmlns:xsi=\\"http://www.w3.org/2001/XMLSchema-instance\\" xmlns=\\"http://datacite.org/schema/kernel-4\\" xsi:schemaLocation=\\"http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd\\">
   <identifier identifierType=\\"DOI\\">12345</identifier>

package/src/libs/doi/__tests__/doi.spec.js

@@ -1,5 +1,7 @@
 import { template, formatBasicAuth } from '../index.js'
 
+vi.mock('ioredis')
+
 describe('DOI minting utils', () => {
   describe('auth()', () => {
     it('returns a base64 basic auth string', () => {

package/src/libs/doi/__tests__/normalize.spec.ts

@@ -1,5 +1,8 @@
+import { vi } from 'vitest'
 import { normalizeDOI } from '../normalize'
 
+vi.mock('ioredis')
+
 describe('DOI normalize utility', () => {
   it('returns null for non-DOI input', () => {
     expect(normalizeDOI('Sphinx of black quartz, judge my vow.')).toBe(null)

package/src/libs/email/__tests__/index.spec.ts

@@ -1,6 +1,8 @@
+import { vi } from 'vitest'
 import { mailjetFormat } from '../index'
 
-jest.mock('../../../config.js')
+vi.mock('ioredis')
+vi.mock('../../../config.js')
 
 describe('Mailjet formatter', () => {
   it('formats a message', () => {

package/src/libs/email/templates/__tests__/__snapshots__/comment-created.spec.ts.snap

@@ -1,6 +1,6 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
+// Vitest Snapshot v1
 
-exports[`email template -> comment created renders with expected arguments 1`] = `
+exports[`email template -> comment created > renders with expected arguments 1`] = `
 "<html>
 <head>
 <style>

package/src/libs/email/templates/__tests__/__snapshots__/dataset-deleted.spec.ts.snap

@@ -1,6 +1,6 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
+// Vitest Snapshot v1
 
-exports[`email template -> comment created renders with expected arguments 1`] = `
+exports[`email template -> comment created > renders with expected arguments 1`] = `
 "<html>
 <head>
 <style>

package/src/libs/email/templates/__tests__/__snapshots__/owner-unsubscribed.spec.ts.snap

@@ -1,6 +1,6 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
+// Vitest Snapshot v1
 
-exports[`email template -> comment created renders with expected arguments 1`] = `
+exports[`email template -> comment created > renders with expected arguments 1`] = `
 "<html>
 <head>
 <style>

package/src/libs/email/templates/__tests__/__snapshots__/snapshot-created.spec.ts.snap

@@ -1,6 +1,6 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
+// Vitest Snapshot v1
 
-exports[`email template -> comment created renders with expected arguments 1`] = `
+exports[`email template -> comment created > renders with expected arguments 1`] = `
 "<html>
 <head>
 <style>

package/src/libs/email/templates/__tests__/__snapshots__/snapshot-reminder.spec.ts.snap

@@ -1,6 +1,6 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
+// Vitest Snapshot v1
 
-exports[`email template -> comment created renders with expected arguments 1`] = `
+exports[`email template -> comment created > renders with expected arguments 1`] = `
 "<html>
 <head>
 <style>

package/src/models/__tests__/ingestDataset.spec.ts

@@ -1,14 +1,16 @@
+import { vi } from 'vitest'
 import IngestDataset from '../ingestDataset'
 
+vi.mock('ioredis')
+
 describe('IngestDataset model', () => {
-  it('IngestDataset model fails if required fields are missing', done => {
+  it('IngestDataset model fails if required fields are missing', () => {
     const model = new IngestDataset()
     model.validate(result => {
       expect(result.name).toEqual('ValidationError')
-      done()
     })
   })
-  it('IngestDataset model URL validation fails with a bad URL', done => {
+  it('IngestDataset model URL validation fails with a bad URL', async () => {
     const badUrlModel = new IngestDataset({
       datasetId: 'ds00000',
       userId: 'b3df6399-d1be-4e07-b997-9f7aa3ed1f8e',
@@ -16,12 +18,11 @@ describe('IngestDataset model', () => {
       imported: false,
       notified: false,
     })
-    badUrlModel.validate(result => {
+    await badUrlModel.validate(result => {
       expect(result.name).toEqual('ValidationError')
-      done()
     })
   })
-  it('IngestDataset model URL validation succeeds with a good URL', done => {
+  it('IngestDataset model URL validation succeeds with a good URL', async () => {
     const goodUrlModel = new IngestDataset({
       datasetId: 'ds00000',
       userId: 'b3df6399-d1be-4e07-b997-9f7aa3ed1f8e',
@@ -29,9 +30,8 @@ describe('IngestDataset model', () => {
       imported: false,
       notified: false,
     })
-    goodUrlModel.validate(result => {
+    await goodUrlModel.validate(result => {
       expect(result).toBe(undefined)
-      done()
     })
   })
 })

package/src/utils/__tests__/datasetOrSnapshot.spec.ts

@@ -1,8 +1,11 @@
+import { vi } from 'vitest'
 import {
   datasetOrSnapshot,
   getDatasetFromSnapshotId,
 } from '../datasetOrSnapshot'
 
+vi.mock('ioredis')
+
 describe('datasetOrSnapshot()', () => {
   it('resolves a dataset object correctly', () => {
     const dataset = {

package/src/utils/__tests__/validateUrl.spec.ts

@@ -1,5 +1,8 @@
+import { vi } from 'vitest'
 import { validateUrl } from '../validateUrl'
 
+vi.mock('ioredis')
+
 describe('validateUrl', () => {
   it('returns true for a regular HTTPS url', () => {
     expect(validateUrl('https://openneuro.org')).toBe(true)

package/tsconfig.json

@@ -3,7 +3,8 @@
   "compilerOptions": {
     "rootDir": "./src",
     "outDir": "./dist",
-    "tsBuildInfoFile": "../../.build-cache/server.tsbuildinfo"
+    "tsBuildInfoFile": "../../.build-cache/server.tsbuildinfo",
+    "types": ["vitest/globals"]
   },
   "include": ["./src"],
   "files": ["./src/lerna.json"],

package/src/__mocks__/mongoose.js

@@ -1,3 +0,0 @@
-import mongoose from 'mongoose'
-
-export default mongoose

package/src/__mocks__/superagent.js

@@ -1,69 +0,0 @@
-// mock for superagent - __mocks__/superagent.js
-class MockResponse {
-  status() {
-    return 200
-  }
-  ok() {
-    return true
-  }
-  body() {
-    return {}
-  }
-  get() {
-    return jest.fn()
-  }
-  toError() {
-    return jest.fn()
-  }
-}
-
-const createRequestStub = obj => jest.fn(() => obj)
-
-function Request() {
-  this.mockResponse = new MockResponse()
-  this.mockDelay = null
-  this.mockError = null
-
-  this.post = createRequestStub(this)
-  this.get = createRequestStub(this)
-  this.send = createRequestStub(this)
-  this.query = createRequestStub(this)
-  this.field = createRequestStub(this)
-  this.set = createRequestStub(this)
-  this.accept = createRequestStub(this)
-  this.timeout = createRequestStub(this)
-  this.then = cb => {
-    return new Promise((resolve, reject) => {
-      if (this.mockError) {
-        return reject(this.mockError)
-      }
-      return resolve(cb(this.mockResponse))
-    })
-  }
-  this.end = jest.fn().mockImplementation(callback => {
-    if (this.mockDelay) {
-      this.delayTimer = setTimeout(
-        callback,
-        0,
-        this.mockError,
-        this.mockResponse,
-      )
-
-      return
-    }
-
-    callback(this.mockError, this.mockResponse)
-  })
-  //expose helper methods for tests to set
-  this.__setMockDelay = boolValue => {
-    this.mockDelay = boolValue
-  }
-  this.__setMockResponse = mockRes => {
-    this.mockResponse = mockRes
-  }
-  this.__setMockError = mockErr => {
-    this.mockError = mockErr
-  }
-}
-
-module.exports = new Request()

package/src/libs/__mocks__/redis.js

@@ -1,5 +0,0 @@
-import Redis from 'ioredis-mock'
-
-const redis = new Redis({})
-
-export { redis }