@openneuro/server 4.20.4 → 4.20.6-alpha.2

package/src/{routes.js → routes.ts}

@@ -1,28 +1,28 @@
 // dependencies ------------------------------------
 
-import express from 'express'
-import * as users from './handlers/users'
-import * as datalad from './handlers/datalad'
-import * as comments from './handlers/comments'
-import { clientConfig } from './handlers/config.js'
-import * as subscriptions from './handlers/subscriptions'
-import verifyUser from './libs/authentication/verifyUser.js'
-import * as google from './libs/authentication/google.js'
-import * as orcid from './libs/authentication/orcid.js'
-import * as jwt from './libs/authentication/jwt'
-import * as auth from './libs/authentication/states.js'
-import * as doi from './handlers/doi'
-import { sitemapHandler } from './handlers/sitemap.js'
-import { reviewerHandler } from './handlers/reviewer'
+import express from "express"
+import * as users from "./handlers/users"
+import * as datalad from "./handlers/datalad"
+import * as comments from "./handlers/comments"
+import { clientConfig } from "./handlers/config"
+import * as subscriptions from "./handlers/subscriptions"
+import verifyUser from "./libs/authentication/verifyUser"
+import * as google from "./libs/authentication/google"
+import * as orcid from "./libs/authentication/orcid"
+import * as jwt from "./libs/authentication/jwt"
+import * as auth from "./libs/authentication/states"
+import * as doi from "./handlers/doi"
+import { sitemapHandler } from "./handlers/sitemap"
+import { reviewerHandler } from "./handlers/reviewer"
 
 const noCache = (req, res, next) => {
-  res.setHeader('Surrogate-Control', 'no-store')
+  res.setHeader("Surrogate-Control", "no-store")
   res.setHeader(
-    'Cache-Control',
-    'no-store, no-cache, must-revalidate, proxy-revalidate',
+    "Cache-Control",
+    "no-store, no-cache, must-revalidate, proxy-revalidate",
   )
-  res.setHeader('Pragma', 'no-cache')
-  res.setHeader('Expires', '0')
+  res.setHeader("Pragma", "no-cache")
+  res.setHeader("Expires", "0")
 
   next()
 }
@@ -30,22 +30,22 @@ const noCache = (req, res, next) => {
 const routes = [
   // Health check --------------------------------
   {
-    method: 'get',
-    url: '/',
+    method: "get",
+    url: "/",
     handler: (req, res) => {
       res.sendStatus(200)
     },
   },
   // React config --------------------------------
   {
-    method: 'get',
-    url: '/config.js',
+    method: "get",
+    url: "/config.js",
     handler: clientConfig,
   },
   // users ---------------------------------------
   {
-    method: 'get',
-    url: '/users/self',
+    method: "get",
+    url: "/users/self",
     middleware: [noCache, jwt.authenticate, auth.authenticated],
     handler: verifyUser,
   },
@@ -53,78 +53,78 @@ const routes = [
   // comments --------------------------------------
 
   {
-    method: 'post',
-    url: '/comments/reply/:commentId/:userId',
+    method: "post",
+    url: "/comments/reply/:commentId/:userId",
     handler: comments.reply,
   },
 
   // subscriptions ----------------------------------------
 
   {
-    method: 'get',
-    url: '/subscriptions/:datasetId',
+    method: "get",
+    url: "/subscriptions/:datasetId",
     handler: subscriptions.getSubscriptions,
   },
   {
-    method: 'get',
-    url: '/subscriptions/:datasetId/:userId',
+    method: "get",
+    url: "/subscriptions/:datasetId/:userId",
     middleware: [noCache],
     handler: subscriptions.checkUserSubscription,
   },
   {
-    method: 'post',
-    url: '/subscriptions/:datasetId',
+    method: "post",
+    url: "/subscriptions/:datasetId",
     middleware: [jwt.authenticate, auth.authenticated],
     handler: subscriptions.create,
   },
   {
-    method: 'delete',
-    url: '/subscriptions/:datasetId/:userId',
+    method: "delete",
+    url: "/subscriptions/:datasetId/:userId",
     middleware: [jwt.authenticate, auth.authenticated],
     handler: subscriptions.deleteSubscription,
   },
   {
-    method: 'delete',
-    url: '/subscriptions/:datasetId',
+    method: "delete",
+    url: "/subscriptions/:datasetId",
     middleware: [jwt.authenticate, auth.authenticated],
     handler: subscriptions.deleteAll,
   },
 
   // dataset doi ----------------------------------------
   {
-    method: 'post',
-    url: '/doi/:datasetId/:snapshotId',
+    method: "post",
+    url: "/doi/:datasetId/:snapshotId",
     middleware: [jwt.authenticate, auth.authenticated],
     handler: doi.createSnapshotDoi,
   },
   {
-    method: 'get',
-    url: '/doi/:datasetId/:snapshotId',
+    method: "get",
+    url: "/doi/:datasetId/:snapshotId",
     handler: doi.getDoi,
   },
 
   // generate CLI API keys ------------------------------
   {
-    method: 'post',
-    url: '/keygen',
+    method: "post",
+    url: "/keygen",
     middleware: [noCache, jwt.authenticate, auth.authenticated],
     handler: users.createAPIKey,
   },
 
   // file routes
   {
-    method: 'get',
-    url: '/datasets/:datasetId/files/:filename',
+    method: "get",
+    url: "/datasets/:datasetId/files/:filename",
     handler: datalad.getFile,
   },
   {
-    method: 'get',
-    url: '/datasets/:datasetId/snapshots/:snapshotId/files/:filename',
+    method: "get",
+    url: "/datasets/:datasetId/snapshots/:snapshotId/files/:filename",
     handler: datalad.getFile,
   },
   {
-    method: 'get',
-    url: '/datasets/:datasetId/objects/:key',
+    method: "get",
+    url: "/datasets/:datasetId/objects/:key",
     handler: datalad.getObject,
   },
 
@@ -132,42 +132,42 @@ const routes = [
 
   // google
   {
-    method: 'get',
-    url: '/auth/google',
+    method: "get",
+    url: "/auth/google",
     middleware: [noCache],
     handler: google.requestAuth,
   },
   {
-    method: 'get',
-    url: '/auth/google/callback',
+    method: "get",
+    url: "/auth/google/callback",
     middleware: [noCache, google.authCallback],
     handler: jwt.authSuccessHandler,
   },
 
   // orcid
   {
-    method: 'get',
-    url: '/auth/orcid',
+    method: "get",
+    url: "/auth/orcid",
     middleware: [noCache],
     handler: orcid.requestAuth,
   },
   {
-    method: 'get',
-    url: '/auth/orcid/callback',
+    method: "get",
+    url: "/auth/orcid/callback",
     middleware: [noCache, orcid.authCallback],
     handler: jwt.authSuccessHandler,
   },
   // Anonymous reviewer access
   {
-    method: 'get',
-    url: '/reviewer/:token',
+    method: "get",
+    url: "/reviewer/:token",
     middleware: [noCache],
     handler: reviewerHandler,
   },
   // sitemap
   {
-    method: 'get',
-    url: '/sitemap',
+    method: "get",
+    url: "/sitemap",
     handler: sitemapHandler,
   },
 ]
@@ -177,7 +177,7 @@ const routes = [
 const router = express.Router()
 
 for (const route of routes) {
-  const arr = route.hasOwnProperty('middleware') ? route.middleware : []
+  const arr = route.hasOwnProperty("middleware") ? route.middleware : []
   arr.unshift(route.url)
   arr.push(route.handler)
   router[route.method](...arr)

package/src/server.ts

@@ -1,15 +1,15 @@
 /** Needs to run before the other imports in Node */
-import apm from 'elastic-apm-node'
+import apm from "elastic-apm-node"
 apm.start({
-  serviceName: 'openneuro-server',
-  cloudProvider: 'none',
+  serviceName: "openneuro-server",
+  cloudProvider: "none",
 })
 
-import { createServer } from 'http'
-import mongoose from 'mongoose'
-import { connect as redisConnect } from './libs/redis'
-import config from './config'
-import { expressApolloSetup } from './app'
+import { createServer } from "http"
+import mongoose from "mongoose"
+import { connect as redisConnect } from "./libs/redis"
+import config from "./config"
+import { expressApolloSetup } from "./app"
 
 const redisConnectionSetup = async () => {
   try {
@@ -31,7 +31,7 @@ void redisConnectionSetup().then(async () => {
   const server = createServer(app)
   server.listen(config.port, () => {
     // eslint-disable-next-line no-console
-    console.log('Server is listening on port ' + config.port)
+    console.log("Server is listening on port " + config.port)
     // Setup GraphQL subscription transport
     //subscriptionServerFactory(server)
   })

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

@@ -1,53 +1,53 @@
-import { vi } from 'vitest'
+import { vi } from "vitest"
 import {
   datasetOrSnapshot,
   getDatasetFromSnapshotId,
-} from '../datasetOrSnapshot'
+} from "../datasetOrSnapshot"
 
-vi.mock('ioredis')
+vi.mock("ioredis")
 
-describe('datasetOrSnapshot()', () => {
-  it('resolves a dataset object correctly', () => {
+describe("datasetOrSnapshot()", () => {
+  it("resolves a dataset object correctly", () => {
     const dataset = {
-      id: 'ds000001',
-      revision: 'abcfdeg',
+      id: "ds000001",
+      revision: "abcfdeg",
       modified: new Date(),
       draft: {
-        id: 'abcfdeg',
+        id: "abcfdeg",
       },
     }
     expect(datasetOrSnapshot(dataset)).toEqual({
-      datasetId: 'ds000001',
-      revision: 'abcfdeg',
+      datasetId: "ds000001",
+      revision: "abcfdeg",
     })
   })
-  it('resolves snapshot objects correctly', () => {
+  it("resolves snapshot objects correctly", () => {
     const snapshot = {
-      id: 'ds000001:1.0.0',
-      tag: '1.0.0',
-      hexsha: 'abcfdeg',
+      id: "ds000001:1.0.0",
+      tag: "1.0.0",
+      hexsha: "abcfdeg",
       modified: new Date(),
-      files: [{ id: '1234', filename: 'dataset_description.json' }],
+      files: [{ id: "1234", filename: "dataset_description.json" }],
     }
     expect(datasetOrSnapshot(snapshot)).toEqual({
-      datasetId: 'ds000001',
-      revision: 'abcfdeg',
+      datasetId: "ds000001",
+      revision: "abcfdeg",
     })
   })
-  it('resolves the snapshot tag only corner case', () => {
+  it("resolves the snapshot tag only corner case", () => {
     const snapshot = {
-      id: 'ds000002:1.0.1',
-      tag: '1.0.1',
+      id: "ds000002:1.0.1",
+      tag: "1.0.1",
       modified: new Date(),
     }
     expect(datasetOrSnapshot(snapshot)).toEqual({
-      datasetId: 'ds000002',
-      revision: '1.0.1',
+      datasetId: "ds000002",
+      revision: "1.0.1",
     })
   })
-  describe('getDatasetFromSnapshotId', () => {
-    it('extracts the datasetId correctly', () => {
-      expect(getDatasetFromSnapshotId('ds000001:1.0.0')).toBe('ds000001')
+  describe("getDatasetFromSnapshotId", () => {
+    it("extracts the datasetId correctly", () => {
+      expect(getDatasetFromSnapshotId("ds000001:1.0.0")).toBe("ds000001")
     })
   })
 })

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

@@ -1,16 +1,16 @@
-import { vi } from 'vitest'
-import { validateUrl } from '../validateUrl'
+import { vi } from "vitest"
+import { validateUrl } from "../validateUrl"
 
-vi.mock('ioredis')
+vi.mock("ioredis")
 
-describe('validateUrl', () => {
-  it('returns true for a regular HTTPS url', () => {
-    expect(validateUrl('https://openneuro.org')).toBe(true)
+describe("validateUrl", () => {
+  it("returns true for a regular HTTPS url", () => {
+    expect(validateUrl("https://openneuro.org")).toBe(true)
   })
-  it('returns false for a regular HTTP url', () => {
-    expect(validateUrl('http://openneuro.org')).toBe(false)
+  it("returns false for a regular HTTP url", () => {
+    expect(validateUrl("http://openneuro.org")).toBe(false)
   })
-  it('returns false for something that is not really a URL', () => {
-    expect(validateUrl('openneuro.org/robots.txt')).toBe(false)
+  it("returns false for something that is not really a URL", () => {
+    expect(validateUrl("openneuro.org/robots.txt")).toBe(false)
   })
 })

package/src/utils/datasetOrSnapshot.ts

@@ -23,7 +23,7 @@ export type DatasetOrSnapshot = HasId | HasSnapshotId
 export function datasetOrSnapshot(
   obj: DatasetOrSnapshot,
 ): DatasetRevisionReference {
-  if ('tag' in obj) {
+  if ("tag" in obj) {
     return {
       datasetId: getDatasetFromSnapshotId(obj.id),
       revision: obj.hexsha || obj.tag,
@@ -38,5 +38,5 @@ export function datasetOrSnapshot(
  * @returns {string} Dataset id portion 'ds000001'
  */
 export function getDatasetFromSnapshotId(snapshotId: string): string {
-  return snapshotId.split(':')[0]
+  return snapshotId.split(":")[0]
 }

package/src/utils/validateUrl.ts

@@ -6,7 +6,7 @@
 export function validateUrl(value: string): boolean {
   try {
     const url = new URL(value)
-    return url.protocol === 'https:'
+    return url.protocol === "https:"
   } catch (err) {
     return false
   }

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

@@ -1,82 +0,0 @@
-import * as changelog from '../changelog.js'
-
-vi.mock('ioredis')
-vi.mock('../../config.js')
-
-describe('changelog editing tools', () => {
-  describe('findVersion()', () => {
-    it('finds the version bounds for a single entry', () => {
-      const newChanges = ['1.0.0 2019-01-01', '  - Initial version']
-      expect(changelog.findVersion(newChanges, '1.0.0')).toEqual([0, 2])
-    })
-    it('returns an empty array when no matching version is found', () => {
-      const newChanges = ['1.0.0 2019-01-01', '  - Initial version']
-      expect(changelog.findVersion(newChanges, '1.0.1')).toEqual([])
-    })
-    it('returns the correct offset for a change in the middle of others', () => {
-      const newChanges = [
-        '2.0.0 2019-02-02',
-        '  - New derivatives',
-        '1.1.0 2019-02-01',
-        '  - Added subjects',
-        '  - Fixed metadata',
-        '1.0.0 2019-01-01',
-        '  - Initial version',
-      ]
-      expect(changelog.findVersion(newChanges, '1.1.0')).toEqual([2, 3])
-    })
-    it('works with fuzzy data', () => {
-      const newChanges = ['I', 'am', 'a', 'banana']
-      expect(changelog.findVersion(newChanges, '1.0.0')).toEqual([])
-    })
-  })
-  describe('spliceChangelog()', () => {
-    it('splices in changes to an existing changelog', () => {
-      const original = '1.0.0 2019-01-01\n  - Initial version\n'
-      const changes = ['Some new change', 'Another new change']
-      const tag = '1.0.0'
-      expect(
-        changelog.spliceChangelog(original, tag, '2019-02-01', changes),
-      ).toEqual(
-        '1.0.0 2019-02-01\n  - Some new change\n  - Another new change\n',
-      )
-    })
-    it('splices correctly when no matching version is found', () => {
-      const original = '1.0.0 2019-01-01\n  - Initial version\n'
-      const changes = ['Some new change']
-      const tag = '1.0.1'
-      expect(
-        changelog.spliceChangelog(original, tag, '2019-02-01', changes),
-      ).toEqual(
-        '1.0.1 2019-02-01\n  - Some new change\n1.0.0 2019-01-01\n  - Initial version\n',
-      )
-    })
-    it('handles fuzzy data', () => {
-      const original = 'abc 123 not a changelog\nnope'
-      const changes = ['Fixed up data']
-      const tag = '1.0.0'
-      expect(
-        changelog.spliceChangelog(original, tag, '2019-02-01', changes),
-      ).toEqual(
-        '1.0.0 2019-02-01\n  - Fixed up data\nabc 123 not a changelog\nnope\n',
-      )
-    })
-    it('works with legacy versions', () => {
-      const original = '00001 1999-12-31\n  - Partying'
-      const changes = ['Bringing dataset into the present day']
-      const tag = '1.0.0'
-      expect(
-        changelog.spliceChangelog(original, tag, '2019-02-01', changes),
-      ).toEqual(
-        '1.0.0 2019-02-01\n  - Bringing dataset into the present day\n00001 1999-12-31\n  - Partying\n',
-      )
-    })
-    it('works if no CHANGES are provided', () => {
-      expect(
-        changelog.spliceChangelog('', '1.0.0', '2019-03-04', [
-          'Initial snapshot',
-        ]),
-      ).toEqual('1.0.0 2019-03-04\n  - Initial snapshot\n')
-    })
-  })
-})

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

@@ -1,109 +0,0 @@
-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
-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()', () => {
-    beforeAll(() => {
-      // Setup MongoDB with mongodb-memory-server
-      connect(globalThis.__MONGO_URI__)
-    })
-    it('resolves to dataset id string', async () => {
-      const user = { id: '1234' }
-      const { id: dsId } = await createDataset(user.id, user, {
-        affirmedDefaced: true,
-        affirmedConsent: true,
-      })
-      expect(dsId).toHaveLength(8)
-      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(user.id, user, {
-        affirmedDefaced: true,
-        affirmedConsent: true,
-      })
-      expect(request.post).toHaveBeenCalledTimes(1)
-      expect(request.post).toHaveBeenCalledWith(
-        expect.stringContaining(`${getDatasetWorker(dsId)}/datasets/`),
-      )
-    })
-  })
-  describe('datasetsFilter()', () => {
-    describe('filterBy: {all: true} ', () => {
-      it('returns the specified match for regular users', () => {
-        const testMatch = { test: 'match' }
-        expect(
-          datasetsFilter({
-            userId: '1234',
-            admin: false,
-            filterBy: { all: true },
-          })(testMatch)[0].$match,
-        ).toBe(testMatch)
-      })
-      it('excludes match argument for admins', () => {
-        const testMatch = { test: 'match' }
-        expect(
-          datasetsFilter({
-            userId: '5678',
-            admin: true,
-            filterBy: { all: true },
-          })(testMatch),
-        ).not.toBe(testMatch)
-      })
-    })
-    describe('filterBy: {invalid: true}', () => {
-      it('returns the correct number of stages', () => {
-        expect(
-          datasetsFilter({ filterBy: { invalid: true } })({}),
-        ).toHaveLength(4)
-      })
-    })
-    describe('filterBy: {invalid: true, public: true}', () => {
-      it('returns the same number of stages as invalid: true', () => {
-        expect(
-          datasetsFilter({ filterBy: { invalid: true, public: true } })({}),
-        ).toHaveLength(4)
-      })
-      it('returns one less stage for admins with all', () => {
-        expect(
-          datasetsFilter({
-            admin: true,
-            filterBy: { invalid: true, public: true, all: true },
-          })({}),
-        ).toHaveLength(3)
-      })
-    })
-    describe('testBlacklist', () => {
-      it('returns false for .bidsignore', () => {
-        expect(testBlacklist('', '.bidsignore')).toBe(false)
-      })
-      it('returns true for .git paths', () => {
-        expect(testBlacklist('.git', 'HEAD')).toBe(true)
-      })
-      it('returns true for root level .DS_Store files', () => {
-        expect(testBlacklist('', '.DS_Store')).toBe(true)
-      })
-      it('returns true for nested .DS_Store files', () => {
-        expect(testBlacklist('sub-01/anat/', '.DS_Store')).toBe(true)
-      })
-      // https://github.com/OpenNeuroOrg/openneuro/issues/2519
-      it('skips ._ prefixed files created by macOS', () => {
-        expect(testBlacklist('', '._.DS_Store')).toBe(true)
-        expect(testBlacklist('stimuli/', '._1002.png')).toBe(true)
-        expect(testBlacklist('stimuli/', 'test._1002.png')).toBe(false)
-      })
-    })
-  })
-})