Merge pull request #2931 from OpenNeuroOrg/server/typescript-fixes

Migrate server code to TypeScript

packages/openneuro-server/src/app.ts

@@ -21,9 +21,9 @@ import Keyv from 'keyv'
 import KeyvRedis from '@keyv/redis'
 import cookieParser from 'cookie-parser'
 import * as jwt from './libs/authentication/jwt'
-import * as auth from './libs/authentication/states.js'
-import { sitemapHandler } from './handlers/sitemap.js'
-import { setupPassportAuth } from './libs/authentication/passport.js'
+import * as auth from './libs/authentication/states'
+import { sitemapHandler } from './handlers/sitemap'
+import { setupPassportAuth } from './libs/authentication/passport'
 import { redis } from './libs/redis'
 import { version } from './lerna.json'
 export { Express } from 'express-serve-static-core'

packages/openneuro-server/src/datalad/__tests__/changelog.spec.js → packages/openneuro-server/src/datalad/__tests__/changelog.spec.ts

@@ -1,7 +1,8 @@
-import * as changelog from '../changelog.js'
+import { vi } from 'vitest'
+import * as changelog from '../changelog'
 
 vi.mock('ioredis')
-vi.mock('../../config.js')
+vi.mock('../../config.ts')
 
 describe('changelog editing tools', () => {
   describe('findVersion()', () => {

packages/openneuro-server/src/datalad/__tests__/dataset.spec.js → packages/openneuro-server/src/datalad/__tests__/dataset.spec.ts

@@ -1,15 +1,15 @@
 import { vi } from 'vitest'
 import request from 'superagent'
-import { createDataset, datasetsFilter, testBlacklist } from '../dataset.js'
+import { createDataset, datasetsFilter, testBlacklist } from '../dataset'
 import { getDatasetWorker } from '../../libs/datalad-service'
 import { connect } from 'mongoose'
 
 // Mock requests to Datalad service
 vi.mock('superagent')
 vi.mock('ioredis')
-vi.mock('../../libs/redis.js')
-vi.mock('../../config.js')
-vi.mock('../../libs/notifications.js')
+vi.mock('../../libs/redis')
+vi.mock('../../config.ts')
+vi.mock('../../libs/notifications')
 
 describe('dataset model operations', () => {
   describe('createDataset()', () => {

packages/openneuro-server/src/datalad/__tests__/description.spec.js → packages/openneuro-server/src/datalad/__tests__/description.spec.ts

@@ -1,12 +1,13 @@
+import { vi } from 'vitest'
 import {
   getDescriptionObject,
   repairDescriptionTypes,
   appendSeniorAuthor,
-} from '../description.js'
+} from '../description'
 
 // Mock requests to Datalad service
 vi.mock('ioredis')
-vi.mock('../../config.js')
+vi.mock('../../config.ts')
 
 describe('datalad dataset descriptions', () => {
   describe('appendSeniorAuthor', () => {
@@ -92,6 +93,7 @@ describe('datalad dataset descriptions', () => {
       global.fetch = vi.fn()
     })
     it('returns the parsed dataset_description.json object', async () => {
+      // @ts-expect-error Fetch mock includes mockResolvedValue
       fetch.mockResolvedValue({
         json: () =>
           Promise.resolve({ Name: 'Balloon Analog Risk-taking Task' }),
@@ -105,6 +107,7 @@ describe('datalad dataset descriptions', () => {
     })
     it('handles a corrupted response', async () => {
       global.fetch = vi.fn()
+      // @ts-expect-error Fetch mock includes mockResolvedValue
       fetch.mockResolvedValue({
         json: () => Promise.reject('JSON could not be parsed'),
         headers: {
@@ -120,6 +123,7 @@ describe('datalad dataset descriptions', () => {
     })
     it('throws an error when nothing is returned', async () => {
       global.fetch = vi.fn()
+      // @ts-expect-error Fetch mock includes mockResolvedValue
       fetch.mockResolvedValue({
         json: () => Promise.reject('JSON could not be parsed'),
         headers: {

packages/openneuro-server/src/datalad/__tests__/files.spec.js → packages/openneuro-server/src/datalad/__tests__/files.spec.ts

@@ -1,3 +1,4 @@
+import { vi } from 'vitest'
 import {
   encodeFilePath,
   decodeFilePath,
@@ -6,7 +7,7 @@ import {
 } from '../files'
 
 vi.mock('ioredis')
-vi.mock('../../config.js')
+vi.mock('../../config.ts')
 
 const filename = 'sub-01/anat/sub-01_T1w.nii.gz'
 
@@ -69,6 +70,7 @@ describe('datalad files', () => {
           size: 1945682,
         },
       ]
+      // @ts-expect-error Test is mocking this
       expect(computeTotalSize(mockFileSizes)).toBe(1957206)
     })
   })

packages/openneuro-server/src/datalad/__tests__/snapshots.spec.js → packages/openneuro-server/src/datalad/__tests__/snapshots.spec.ts

@@ -1,8 +1,8 @@
 import { vi } from 'vitest'
 vi.mock('ioredis')
 import request from 'superagent'
-import { createDataset } from '../dataset.js'
-import { createSnapshot } from '../snapshots.js'
+import { createDataset } from '../dataset'
+import { createSnapshot } from '../snapshots'
 import { getDatasetWorker } from '../../libs/datalad-service'
 import { connect } from 'mongoose'
 
@@ -17,11 +17,11 @@ vi.mock('../../libs/redis.js', () => ({
   },
 }))
 // Mock draft files calls
-vi.mock('../draft.js', () => ({
+vi.mock('../draft.ts', () => ({
   updateDatasetRevision: () => () => Promise.resolve(),
 }))
-vi.mock('../../config.js')
-vi.mock('../../libs/notifications.js')
+vi.mock('../../config.ts')
+vi.mock('../../libs/notifications.ts')
 
 describe('snapshot model operations', () => {
   describe('createSnapshot()', () => {

packages/openneuro-server/src/datalad/changelog.js → packages/openneuro-server/src/datalad/changelog.ts

@@ -1,5 +1,5 @@
 import format from 'date-fns/format'
-import { addFileString, commitFiles } from './dataset.js'
+import { addFileString, commitFiles } from './dataset'
 import { getDatasetWorker } from '../libs/datalad-service'
 
 /**

packages/openneuro-server/src/datalad/dataset.js → packages/openneuro-server/src/datalad/dataset.ts

@@ -7,14 +7,15 @@ import request from 'superagent'
 import requestNode from 'request'
 import objectHash from 'object-hash'
 import { Readable } from 'stream'
+import * as Mongoose from 'mongoose'
 import config from '../config'
-import * as subscriptions from '../handlers/subscriptions.js'
+import * as subscriptions from '../handlers/subscriptions'
 import { generateDataladCookie } from '../libs/authentication/jwt'
 import { redis } from '../libs/redis'
 import CacheItem, { CacheType } from '../cache/item'
-import { updateDatasetRevision } from './draft.js'
+import { updateDatasetRevision } from './draft'
 import { fileUrl, getFileName, encodeFilePath, filesUrl } from './files'
-import { getAccessionNumber } from '../libs/dataset.js'
+import { getAccessionNumber } from '../libs/dataset'
 import Dataset from '../models/dataset'
 import Metadata from '../models/metadata'
 import Permission from '../models/permission'
@@ -119,7 +120,7 @@ export const cacheDatasetConnection = options => connectionArguments => {
  * @param {object} match MongoDB $match aggregate
  * @returns {Array<object>} Array of MongoDB aggregate pipelines
  */
-const aggregateArraySetup = match => [{ $match: match }]
+const aggregateArraySetup = (match): Mongoose.Expression => [{ $match: match }]
 
 /**
  * Add any filter steps based on the filterBy options provided
@@ -157,7 +158,7 @@ export const datasetsFilter = options => match => {
     )
     return aggregates
   }
-  const filterMatch = {}
+  const filterMatch: Mongoose.Expression = {}
   if ('filterBy' in options) {
     const filters = options.filterBy
     if (

packages/openneuro-server/src/datalad/description.js → packages/openneuro-server/src/datalad/description.ts

@@ -3,8 +3,8 @@
  */
 import config from '../config'
 import request from 'superagent'
-import { redis } from '../libs/redis.js'
-import { commitFiles } from './dataset.js'
+import { redis } from '../libs/redis'
+import { commitFiles } from './dataset'
 import { fileUrl } from './files'
 import { generateDataladCookie } from '../libs/authentication/jwt'
 import { getDatasetWorker } from '../libs/datalad-service'

packages/openneuro-server/src/datalad/draft.js → packages/openneuro-server/src/datalad/draft.ts

@@ -3,7 +3,6 @@
  */
 import request from 'superagent'
 import Dataset from '../models/dataset'
-import publishDraftUpdate from '../graphql/utils/publish-draft-update.js'
 import { getDatasetWorker } from '../libs/datalad-service'
 
 export const getDraftRevision = async datasetId => {
@@ -19,9 +18,7 @@ export const updateDatasetRevision = (datasetId, gitRef) => {
   /**
    * Update the revision modified time in a draft on changes
    */
-  return Dataset.updateOne({ id: datasetId }, { modified: new Date() })
-    .exec()
-    .then(() => publishDraftUpdate(datasetId, gitRef))
+  return Dataset.updateOne({ id: datasetId }, { modified: new Date() }).exec()
 }
 
 /**

packages/openneuro-server/src/datalad/snapshots.js → packages/openneuro-server/src/datalad/snapshots.ts

@@ -5,19 +5,19 @@ import request from 'superagent'
 import { reindexDataset } from '../elasticsearch/reindex-dataset'
 import { redis, redlock } from '../libs/redis'
 import CacheItem, { CacheType } from '../cache/item'
-import config from '../config.js'
+import config from '../config'
 import {
   updateDatasetName,
   snapshotCreationComparison,
-} from '../graphql/resolvers/dataset.js'
-import { description } from '../graphql/resolvers/description.js'
-import doiLib from '../libs/doi/index.js'
+} from '../graphql/resolvers/dataset'
+import { description } from '../graphql/resolvers/description'
+import doiLib from '../libs/doi/index'
 import { getFiles } from './files'
 import { generateDataladCookie } from '../libs/authentication/jwt'
 import notifications from '../libs/notifications'
 import Dataset from '../models/dataset'
-import Snapshot from '../models/snapshot'
-import { updateDatasetRevision } from './draft.js'
+import Snapshot, { SnapshotDocument } from '../models/snapshot'
+import { updateDatasetRevision } from './draft'
 import { getDatasetWorker } from '../libs/datalad-service'
 import { join } from 'path'
 
@@ -94,7 +94,7 @@ const postSnapshot = async (
  * @param {string} datasetId Dataset accession number
  * @returns {Promise<import('../models/snapshot').SnapshotDocument[]>}
  */
-export const getSnapshots = datasetId => {
+export const getSnapshots = (datasetId): Promise<SnapshotDocument[]> => {
   const url = `${getDatasetWorker(datasetId)}/datasets/${datasetId}/snapshots`
   return request
     .get(url)
@@ -194,7 +194,10 @@ export const deleteSnapshot = (datasetId, tag) => {
  * @param {string} commitRef Tag name to retrieve
  * @returns {Promise<import('../models/snapshot').SnapshotDocument>}
  */
-export const getSnapshot = (datasetId, commitRef) => {
+export const getSnapshot = (
+  datasetId,
+  commitRef,
+): Promise<SnapshotDocument> => {
   const url = `${getDatasetWorker(
     datasetId,
   )}/datasets/${datasetId}/snapshots/${commitRef}`

packages/openneuro-server/src/elasticsearch/elastic-client.js → packages/openneuro-server/src/elasticsearch/elastic-client.ts

@@ -1,4 +1,4 @@
-import config from '../config.js'
+import config from '../config'
 import { Client } from '@elastic/elasticsearch'
 
 const elasticConfig = {

packages/openneuro-server/src/elasticsearch/reindex-dataset.ts

@@ -1,4 +1,4 @@
-import config from '../config.js'
+import config from '../config'
 import { indexDataset, queryForIndex, indexingToken } from '@openneuro/search'
 import { elasticClient } from './elastic-client'
 import {

packages/openneuro-server/src/graphql/__tests__/__snapshots__/permissions.spec.ts.snap

@@ -0,0 +1,5 @@
+// Vitest Snapshot v1, https://vitest.dev/guide/snapshot.html
+
+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."`;

packages/openneuro-server/src/graphql/__tests__/permissions.spec.js → packages/openneuro-server/src/graphql/__tests__/permissions.spec.ts

@@ -1,3 +1,4 @@
+import { vi } from 'vitest'
 import {
   datasetReadQuery,
   checkPermissionLevel,
@@ -95,12 +96,17 @@ describe('resolver permissions helpers', () => {
   describe('checkDatasetAdmin()', () => {
     it('resolves to false for anonymous users', () => {
       return expect(
-        checkDatasetAdmin('ds000001', null, null, false),
+        checkDatasetAdmin('ds000001', null, null, { checkExists: false }),
       ).rejects.toThrowErrorMatchingSnapshot()
     })
     it('resolves to true for admins', () => {
       return expect(
-        checkDatasetAdmin('ds000001', '1234', { admin: true }, false),
+        checkDatasetAdmin(
+          'ds000001',
+          '1234',
+          { admin: true },
+          { checkExists: false },
+        ),
       ).resolves.toBe(true)
     })
   })

packages/openneuro-server/src/graphql/permissions.js → packages/openneuro-server/src/graphql/permissions.ts

@@ -1,4 +1,4 @@
-import config from '../config.js'
+import config from '../config'
 import { GraphQLError } from 'graphql'
 import Permission from '../models/permission'
 import Dataset from '../models/dataset'

packages/openneuro-server/src/graphql/resolvers/__tests__/dataset-search.spec.js → packages/openneuro-server/src/graphql/resolvers/__tests__/dataset-search.spec.ts

@@ -1,12 +1,13 @@
+import { vi } from 'vitest'
 import {
   encodeCursor,
   decodeCursor,
   elasticRelayConnection,
 } from '../dataset-search'
 
 vi.mock('ioredis')
-vi.mock('../../../elasticsearch/elastic-client.js')
-vi.mock('../../../config.js')
+vi.mock('../../../elasticsearch/elastic-client.ts')
+vi.mock('../../../config.ts')
 
 describe('dataset search resolvers', () => {
   describe('encodeCursor()', () => {
@@ -46,6 +47,7 @@ describe('dataset search resolvers', () => {
           hasPreviousPage: false,
         },
       }
+      // @ts-expect-error Mock version does not use all arguments
       const connection = await elasticRelayConnection(emptyApiResponse, {
         dataset: vi.fn(),
       })

packages/openneuro-server/src/graphql/resolvers/__tests__/dataset.spec.js → packages/openneuro-server/src/graphql/resolvers/__tests__/dataset.spec.ts

@@ -5,8 +5,8 @@ import * as ds from '../dataset'
 
 vi.mock('superagent')
 vi.mock('ioredis')
-vi.mock('../../../config.js')
-vi.mock('../../../libs/notifications.js')
+vi.mock('../../../config.ts')
+vi.mock('../../../libs/notifications.ts')
 
 describe('dataset resolvers', () => {
   beforeAll(() => {
@@ -40,9 +40,9 @@ describe('dataset resolvers', () => {
     })
     it('sorts array of objects by the "created" property as strings', () => {
       const testArray = [
-        { id: 2, created: '2018-11-20T00:05:43.473Z' },
-        { id: 1, created: '2018-11-19T00:05:43.473Z' },
-        { id: 3, created: '2018-11-23T00:05:43.473Z' },
+        { id: 2, created: '2018-11-20T00:05:43.473Z', tag: '2.0.0' },
+        { id: 1, created: '2018-11-19T00:05:43.473Z', tag: '1.0.0' },
+        { id: 3, created: '2018-11-23T00:05:43.473Z', tag: '3.0.0' },
       ]
       const sorted = testArray.sort(ds.snapshotCreationComparison)
       expect(sorted[0].id).toBe(1)

packages/openneuro-server/src/graphql/resolvers/__tests__/permssions.spec.js → packages/openneuro-server/src/graphql/resolvers/__tests__/permssions.spec.ts

@@ -1,3 +1,4 @@
+import { vi } from 'vitest'
 import { updatePermissions } from '../permissions'
 
 vi.mock('ioredis')
@@ -22,7 +23,7 @@ describe('permissions resolvers', () => {
         await updatePermissions(
           {},
           { datasetId: 'ds01234', userEmail: 'fake@test.com' },
-          {},
+          { user: '1234', userInfo: { id: '1234' } },
         )
       } catch (err) {
         error = err

packages/openneuro-server/src/graphql/resolvers/__tests__/snapshots.spec.js → packages/openneuro-server/src/graphql/resolvers/__tests__/snapshots.spec.ts

@@ -1,7 +1,8 @@
-import { matchKnownObjects, filterLatestSnapshot } from '../snapshots.js'
+import { vi } from 'vitest'
+import { matchKnownObjects, filterLatestSnapshot } from '../snapshots'
 
 vi.mock('ioredis')
-vi.mock('../../../config.js')
+vi.mock('../../../config.ts')
 
 describe('snapshot resolvers', () => {
   describe('matchKnownObjects()', () => {

packages/openneuro-server/src/graphql/resolvers/__tests__/user.spec.js → packages/openneuro-server/src/graphql/resolvers/__tests__/user.spec.ts

@@ -1,3 +1,4 @@
+import { vi } from 'vitest'
 import { users } from '../user.js'
 
 vi.mock('ioredis')

packages/openneuro-server/src/graphql/resolvers/comment.js → packages/openneuro-server/src/graphql/resolvers/comment.ts

@@ -1,5 +1,5 @@
 import Comment from '../../models/comment'
-import notifications from '../../libs/notifications.js'
+import notifications from '../../libs/notifications'
 import { user } from './user.js'
 import { checkAdmin } from '../permissions'