@openneuro/server 4.20.5 → 4.20.6-alpha.2

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

@@ -1,34 +0,0 @@
-import { updatePermissions } from '../permissions'
-
-vi.mock('ioredis')
-vi.mock('../../permissions', () => ({
-  checkDatasetAdmin: async () => Promise.resolve(),
-}))
-
-const mockExec = vi.fn()
-
-vi.mock('../../../models/user', () => ({
-  find: () => ({
-    exec: mockExec,
-  }),
-}))
-
-describe('permissions resolvers', () => {
-  describe('updatePermissions()', () => {
-    it('throws an error when no users are found', async () => {
-      mockExec.mockResolvedValue([])
-      let error
-      try {
-        await updatePermissions(
-          {},
-          { datasetId: 'ds01234', userEmail: 'fake@test.com' },
-          {},
-        )
-      } catch (err) {
-        error = err
-      }
-
-      return expect(error).toBeInstanceOf(Error)
-    })
-  })
-})

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

@@ -1,58 +0,0 @@
-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', () => {
-      expect(
-        matchKnownObjects({
-          ReferencesAndLinks: [
-            '10.18112/openneuro.ds000001.v1.0.0',
-            '10.15154/1503209',
-          ],
-        }).sort(),
-      ).toEqual([
-        {
-          id: '10.18112/openneuro.ds000001.v1.0.0',
-        },
-        {
-          id: '10.15154/1503209',
-          source: 'NDA',
-          type: 'dataset',
-        },
-      ])
-    })
-  })
-  describe('filterLatestSnapshot()', () => {
-    it('returns the latest snapshot', () => {
-      const testSnapshots = [
-        {
-          id: 'ds000247:00002',
-          created: '2018-07-18T02:27:39.000Z',
-          tag: '00002',
-        },
-        {
-          id: 'ds000247:00001',
-          created: '2018-07-18T02:35:37.000Z',
-          tag: '00001',
-        },
-        {
-          id: 'ds000247:1.0.0',
-          created: '2021-07-05T15:58:18.000Z',
-          tag: '1.0.0',
-        },
-        {
-          id: 'ds000247:1.0.1',
-          created: '2021-08-25T23:37:53.000Z',
-          tag: '1.0.1',
-        },
-      ]
-      expect(filterLatestSnapshot(testSnapshots)).toBe('1.0.1')
-    })
-    it('returns null with no snapshots', () => {
-      expect(filterLatestSnapshot([])).toBeNull()
-    })
-  })
-})

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

@@ -1,17 +0,0 @@
-import { users } from '../user.js'
-
-vi.mock('ioredis')
-
-describe('user resolvers', () => {
-  describe('users()', () => {
-    it('throws an error for non-admins', () => {
-      expect(
-        users(
-          null,
-          { id: '3311cfe8-9764-434d-b80e-1b1ee72c686d' },
-          { userInfo: {} },
-        ),
-      ).rejects.toEqual(new Error('You must be a site admin to retrieve users'))
-    })
-  })
-})

package/src/graphql/resolvers/description.js

@@ -1,29 +0,0 @@
-/**
- * Resolver implementation for dataset_description.json
- */
-import { setDescription } from '../../datalad/description.js'
-import { checkDatasetWrite } from '../permissions.js'
-export { description } from '../../datalad/description.js'
-import pubsub from '../pubsub.js'
-
-export const updateDescription = (
-  obj,
-  { datasetId, field, value },
-  { user, userInfo },
-) => {
-  return checkDatasetWrite(datasetId, user, userInfo)
-    .then(() => setDescription(datasetId, userInfo, { [field]: value }))
-    .then(description => {
-      pubsub.publish('draftUpdated', {
-        datasetId: description.id,
-        draftUpdated: {
-          draft: {
-            description,
-          },
-        },
-      })
-      return description
-    })
-}
-
-export const updateDescriptionList = updateDescription

package/src/graphql/resolvers/history.js

@@ -1,11 +0,0 @@
-import { getDatasetWorker } from '../../libs/datalad-service.js'
-
-export const history = async obj => {
-  const datasetId = obj.id
-  const historyUrl = `http://${getDatasetWorker(
-    datasetId,
-  )}/datasets/${datasetId}/history`
-  const resp = await fetch(historyUrl)
-  const { log } = await resp.json()
-  return log
-}

package/src/graphql/resolvers/index.js

@@ -1,25 +0,0 @@
-import { GraphQLDate, GraphQLTime, GraphQLDateTime } from 'graphql-iso-date'
-import GraphQLBigInt from 'graphql-bigint'
-import Query from './query.js'
-import Mutation from './mutation.js'
-import Dataset from './dataset.js'
-import Draft from './draft.js'
-import Snapshot from './snapshots.js'
-import User from './user.js'
-import Comment from './comment.js'
-
-export default {
-  // Scalars
-  Date: GraphQLDate,
-  Time: GraphQLTime,
-  DateTime: GraphQLDateTime,
-  BigInt: GraphQLBigInt,
-  // Complex types
-  Query,
-  Mutation,
-  User,
-  Dataset,
-  Draft,
-  Snapshot,
-  Comment,
-}

package/src/graphql/resolvers/publish.js

@@ -1,17 +0,0 @@
-import config from '../../config'
-import request from 'superagent'
-import { updatePublic } from '../../datalad/dataset.js'
-import { checkDatasetWrite } from '../permissions.js'
-import { generateDataladCookie } from '../../libs/authentication/jwt'
-import { getDatasetWorker } from '../../libs/datalad-service'
-
-export const publishDataset = (obj, { datasetId }, { user, userInfo }) => {
-  return checkDatasetWrite(datasetId, user, userInfo).then(async () => {
-    await updatePublic(datasetId, true)
-    const uri = `${getDatasetWorker(datasetId)}/datasets/${datasetId}/publish`
-    return await request
-      .post(uri)
-      .set('Cookie', generateDataladCookie(config)(userInfo))
-      .then(() => true)
-  })
-}

package/src/graphql/resolvers/query.js

@@ -1,21 +0,0 @@
-/**
- * Top level query
- */
-import { dataset, datasets } from './dataset.js'
-import { snapshot, participantCount } from './snapshots.js'
-import { user, users } from './user.js'
-import { flaggedFiles } from './flaggedFiles'
-import { publicMetadata } from './metadata'
-
-const Query = {
-  dataset,
-  datasets,
-  user,
-  users,
-  snapshot,
-  participantCount,
-  flaggedFiles,
-  publicMetadata,
-}
-
-export default Query

package/src/graphql/resolvers/subscriptions.js

@@ -1,81 +0,0 @@
-import pubsub from '../pubsub.js'
-
-import { withFilter } from 'graphql-subscriptions'
-
-/**
- * Filter subscription to a specific dataset
- * @param {object} payload
- * @param {object} variables
- * @returns {boolean}
- */
-const filterDatasetId = (payload, variables) => {
-  const { datasetId, datasetIds } = variables
-  if (datasetId) return datasetId === payload.datasetId
-  if (datasetIds) return datasetIds.includes(payload.datasetId)
-  return false
-}
-
-export const datasetDeleted = () => ({
-  type: 'ID!',
-  subscribe: withFilter(
-    () => pubsub.asyncIterator('datasetDeleted'),
-    filterDatasetId,
-  ),
-  args: {
-    datasetIds: '[ID!]',
-  },
-})
-
-export const snapshotsUpdated = {
-  type: 'Dataset',
-  subscribe: withFilter(
-    () => pubsub.asyncIterator('snapshotsUpdated'),
-    filterDatasetId,
-  ),
-  args: {
-    datasetId: 'ID!',
-  },
-}
-
-export const draftUpdated = {
-  type: 'Dataset',
-  subscribe: withFilter(
-    () => pubsub.asyncIterator('draftUpdated'),
-    filterDatasetId,
-  ),
-  args: {
-    datasetId: 'ID!',
-  },
-}
-
-export const permissionsUpdated = {
-  type: 'Dataset',
-  subscribe: withFilter(
-    () => pubsub.asyncIterator('permissionsUpdated'),
-    filterDatasetId,
-  ),
-  args: {
-    datasetIds: '[ID!]',
-  },
-}
-
-export const filesUpdated = {
-  type: 'FilesUpdate',
-  subscribe: withFilter(
-    () => pubsub.asyncIterator('filesUpdated'),
-    filterDatasetId,
-  ),
-  args: {
-    datasetId: 'ID!',
-  },
-}
-
-const Subscription = {
-  datasetDeleted,
-  snapshotsUpdated,
-  permissionsUpdated,
-  draftUpdated,
-  filesUpdated,
-}
-
-export default Subscription

package/src/graphql/utils/publish-draft-update.js

@@ -1,13 +0,0 @@
-import pubsub from '../pubsub'
-
-export default (datasetId, revision) => {
-  pubsub.publish('draftUpdated', {
-    datasetId: datasetId,
-    draftUpdated: {
-      __typename: 'Dataset',
-      id: datasetId,
-      head: revision,
-      modified: new Date(), // Set date to now
-    },
-  })
-}

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

@@ -1,24 +0,0 @@
-import jwt from 'jsonwebtoken'
-import { apiKeyFactory } from '../apikey.js'
-import config from '../../config.js'
-
-vi.mock('ioredis')
-vi.mock('../../config.js')
-
-const userMock = {
-  id: '1337',
-  name: 'Total Poser',
-  email: 'porkchopsandwich@gijoe.com',
-  admin: true,
-  provider: 'google',
-}
-
-describe('util/apikey.js', () => {
-  describe('apiKeyFactory', () => {
-    it('produces a valid JWT', () => {
-      const token = jwt.verify(apiKeyFactory(userMock), config.auth.jwt.secret)
-      expect(token.sub).toEqual(userMock.id)
-      expect(token.email).toEqual(userMock.email)
-    })
-  })
-})

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

@@ -1,26 +0,0 @@
-import { hashDatasetToRange } from '../datalad-service'
-
-vi.mock('ioredis')
-
-describe('datalad-service utils', () => {
-  describe('hashDatasetToRange()', () => {
-    it('is stable across a range of datasets', () => {
-      const range = 8
-      expect(hashDatasetToRange('ds000001', range)).toBe(4)
-      expect(hashDatasetToRange('ds000002', range)).toBe(5)
-      expect(hashDatasetToRange('ds000003', range)).toBe(4)
-      expect(hashDatasetToRange('ds000004', range)).toBe(6)
-      expect(hashDatasetToRange('ds001734', range)).toBe(1)
-      expect(hashDatasetToRange('ds001919', range)).toBe(6)
-    })
-    it('is comparable with a small range (4)', () => {
-      const range = 4
-      expect(hashDatasetToRange('ds000001', range)).toBe(0)
-      expect(hashDatasetToRange('ds000002', range)).toBe(1)
-      expect(hashDatasetToRange('ds000003', range)).toBe(0)
-      expect(hashDatasetToRange('ds000004', range)).toBe(2)
-      expect(hashDatasetToRange('ds001734', range)).toBe(1)
-      expect(hashDatasetToRange('ds001919', range)).toBe(2)
-    })
-  })
-})

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

@@ -1,23 +0,0 @@
-import User from '../../../models/user'
-import { addJWT } from '../jwt'
-
-vi.mock('ioredis')
-vi.mock('../../../config.js')
-vi.unmock('mongoose')
-
-describe('jwt auth', () => {
-  describe('addJWT()', () => {
-    it('Extends a User model with a valid token', () => {
-      const config = {
-        auth: {
-          jwt: {
-            secret: '1234',
-          },
-        },
-      }
-      const user = User({ email: 'test@example.com' })
-      const obj = addJWT(config)(user)
-      expect(obj).toHaveProperty('token')
-    })
-  })
-})

package/src/libs/authentication/globus.js

@@ -1,11 +0,0 @@
-import passport from 'passport'
-
-export const requestAuth = passport.authenticate('globus', {
-  scope: ['profile', 'email', 'openid'],
-  session: false,
-})
-
-export const authCallback = passport.authenticate('globus', {
-  failureRedirect: '/',
-  session: false,
-})

package/src/libs/authentication/google.js

@@ -1,19 +0,0 @@
-import passport from 'passport'
-
-export const requestAuth = (req, res, next) => (
-  passport.authenticate('google', {
-    scope: [
-      'https://www.googleapis.com/auth/userinfo.email',
-      'https://www.googleapis.com/auth/userinfo.profile',
-    ],
-    session: false,
-    accessType: 'offline',
-    prompt: 'consent',
-    state: req.query.redirectPath || null
-  })(req, res, next)
-)
-
-export const authCallback = passport.authenticate('google', {
-  failureRedirect: '/',
-  session: false,
-})

package/src/libs/bidsId.js

@@ -1,68 +0,0 @@
-/**
- * Hex
- *
- * Utils for dealing with hex encoding
- */
-export default {
-  hexToASCII(hexString) {
-    const hex = hexString.toString()
-    let str = ''
-    for (let n = 0; n < hex.length; n += 2) {
-      str += String.fromCharCode(parseInt(hex.substr(n, 2), 16))
-    }
-    return str
-  },
-
-  hexFromASCII(string) {
-    return string
-      .split('')
-      .map(c => {
-        return ('0' + c.charCodeAt(0).toString(16)).slice(-2)
-      })
-      .join('')
-  },
-
-  encodeId(id) {
-    if (/ds\d{6}/.test(id)) {
-      return this.hexFromASCII('    ' + id)
-    } else if (/\d{6}-\d{5}/.test(id)) {
-      return this.hexFromASCII(id)
-    } else {
-      return id
-    }
-  },
-
-  decodeId(id) {
-    const decodedId = this.hexToASCII(id)
-    if (/\s{4}ds\d{6}/.test(decodedId)) {
-      return decodedId.slice(4)
-    } else if (/\d{6}-\d{5}/.test(decodedId)) {
-      return decodedId.slice(7)
-    }
-    return id
-  },
-
-  decode(id) {
-    const decodedId = this.hexToASCII(id)
-    let datasetId = null
-    let tag = null
-    // decodes the two different formats of storing dataset + snapshot tag
-    if (/\s{4}ds\d{6}/.test(decodedId)) {
-      datasetId = decodedId.slice(4)
-    } else if (/\d{6}-\d{5}/.test(decodedId)) {
-      tag = decodedId.slice(7)
-      datasetId = 'ds' + decodedId.slice(0, 6)
-    } else {
-      // handles all these old dataset ids that start with 57 or 58
-      if (id.startsWith('57') || id.startsWith('58')) {
-        datasetId = id
-      } else {
-        // if the id is of the proper length but has no ds, add ds.
-        // otherwise, add it is short and needs a 0 as well
-        const beginning = id.length == 6 ? 'ds' : 'ds0'
-        datasetId = beginning + id
-      }
-    }
-    return { datasetId, tag }
-  },
-}

package/src/libs/dataset.js

@@ -1,9 +0,0 @@
-import { getNext } from './counter'
-
-/**
- * Returns the next accession number string
- */
-export async function getAccessionNumber() {
-  const datasetNumber = (await getNext('datasets')) + 1000
-  return `ds${('000000' + datasetNumber).substr(-6, 6)}`
-}

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

@@ -1,24 +0,0 @@
-import { template, formatBasicAuth } from '../index.js'
-
-vi.mock('ioredis')
-
-describe('DOI minting utils', () => {
-  describe('auth()', () => {
-    it('returns a base64 basic auth string', () => {
-      const doiConfig = { username: 'test', password: '12345' }
-      expect(formatBasicAuth(doiConfig)).toBe('Basic dGVzdDoxMjM0NQ==')
-    })
-  })
-  describe('template()', () => {
-    it('accepts expected arguments', () => {
-      const context = {
-        doi: '12345',
-        creators: ['A. User', 'B. User'],
-        title: 'Test Dataset',
-        year: '1999',
-        resourceType: 'fMRI',
-      }
-      expect(template(context)).toMatchSnapshot()
-    })
-  })
-})

package/src/libs/redis-pubsub.js

@@ -1,5 +0,0 @@
-import { RedisPubSub } from 'graphql-redis-subscriptions'
-
-const pubsubFactory = options => new RedisPubSub(options)
-
-export default pubsubFactory

package/src/libs/request.js

@@ -1,155 +0,0 @@
-import request from 'request'
-
-/**
- * Parse Options
- *
- * Normalizes request options.
- */
-function parseOptions(req, options) {
-  if (options.query) {
-    req.qs = options.query
-  }
-  if (options.body) {
-    req.json = options.body
-  }
-  if (options.hasOwnProperty('encoding')) {
-    req.encoding = options.encoding
-  }
-  if (options.headers) {
-    for (const key in options.headers) {
-      req.headers[key] = options.headers[key]
-    }
-  }
-  return req
-}
-
-/**
- * Handle Request
- *
- * Processes all requests before they fire.
- */
-function handleRequest(url, options, callback) {
-  let req = {
-    url: url,
-    headers: {},
-    qs: {},
-    json: {},
-  }
-
-  req = parseOptions(req, options)
-  callback(req)
-}
-
-/**
- * Handle Response
- *
- * Process all responses before they return
- * to the callback.
- */
-function handleResponse(err, res, callback) {
-  callback(err, res)
-}
-
-/**
- * Request
- *
- * A wrapper of npm 'request' to allow for
- * genericizing request and response manipulations.
- */
-export default {
-  get(url, options, callback) {
-    handleRequest(url, options, req => {
-      request.get(req, (err, res) => {
-        handleResponse(err, res, callback)
-      })
-    })
-  },
-
-  /**
-   * GET CACHE
-   *
-   * Functions the same as request but takes a
-   * cache function, checks to see if the response is
-   * already cached. If so, responds with the cached data.
-   * If not, stores the response in the cache before responding.
-   */
-  getCache(url, cache, options, callback) {
-    handleRequest(url, options, req => {
-      cache.get(req, (err, res1) => {
-        if (res1) {
-          handleResponse(err, res1, callback)
-        } else {
-          request.get(req, (err, res2) => {
-            if (err) {
-              handleResponse(err, res2, callback)
-            } else {
-              const data = res2.body
-              cache.store(data, () => {
-                handleResponse(err, res2, callback)
-              })
-            }
-          })
-        }
-      })
-    })
-  },
-
-  postCache(url, cache, options, callback) {
-    handleRequest(url, options, req => {
-      request.post(req, (err, res) => {
-        if (err) {
-          handleResponse(err, res, callback)
-        } else {
-          const data = req.json
-          cache.store(data, () => {
-            handleResponse(err, res, callback)
-          })
-        }
-      })
-    })
-  },
-
-  /**
-   * GET PROXY
-   *
-   * Functions the same as a get request but takes a
-   * response object instead of a callback and pipes
-   * the request response to the response object.
-   */
-  getProxy(url, options, res) {
-    handleRequest(url, options, req => {
-      request
-        .get(req)
-        .on('data', resp => {
-          if (options.status) {
-            resp.statusCode = options.status
-          }
-        })
-        .pipe(res)
-    })
-  },
-
-  post(url, options, callback) {
-    handleRequest(url, options, req => {
-      request.post(req, (err, res) => {
-        handleResponse(err, res, callback)
-      })
-    })
-  },
-
-  put(url, options, callback) {
-    handleRequest(url, options, req => {
-      request.put(req, (err, res) => {
-        handleResponse(err, res, callback)
-      })
-    })
-  },
-
-  del(url, options, callback) {
-    handleRequest(url, options, req => {
-      request.del(req, (err, res) => {
-        handleResponse(err, res, callback)
-      })
-    })
-  },
-}