@openneuro/server 5.0.0 → 5.1.1

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

@@ -12,7 +12,7 @@ import mongoose, { Types } from "mongoose"
 import User from "../../../models/user"
 import DatasetEvent from "../../../models/datasetEvents"
 import { notifications, user, users } from "../user.js"
-import type { GraphQLContext } from "../user.js"
+import type { GraphQLContext } from "../../builder"
 
 vi.mock("ioredis")
 
@@ -108,13 +108,25 @@ const testUsersSeedData = [
 ]
 
 // Admin context for tests
-const adminContext: GraphQLContext = {
-  userInfo: { userId: "admin-user", admin: true, username: "adminUser" },
-}
+const adminContext = {
+  user: "admin-user",
+  userInfo: {
+    id: "admin-user",
+    userId: "admin-user",
+    admin: true,
+    username: "adminUser",
+  },
+} as GraphQLContext
 // Non-admin context for tests
-const nonAdminContext: GraphQLContext = {
-  userInfo: { userId: "normal-user", admin: false, username: "normalUser" },
-}
+const nonAdminContext = {
+  user: "normal-user",
+  userInfo: {
+    id: "normal-user",
+    userId: "normal-user",
+    admin: false,
+    username: "normalUser",
+  },
+} as GraphQLContext
 
 describe("user resolvers", () => {
   beforeAll(async () => {
@@ -392,14 +404,26 @@ describe("user resolvers", () => {
       const result = await notifications(
         { id: "reviewer" },
         null,
-        { userInfo: { reviewer: true, admin: false, blocked: false } },
+        {
+          userInfo: {
+            id: "reviewer",
+            userId: "reviewer",
+            reviewer: true,
+            admin: false,
+            blocked: false,
+          },
+        } as GraphQLContext,
       )
       expect(result).toEqual([])
     })
 
     it("does not crash when userInfo is undefined", async () => {
       await expect(
-        notifications({ id: "u1" }, null, { userInfo: undefined }),
+        notifications(
+          { id: "u1" },
+          null,
+          { userInfo: undefined } as GraphQLContext,
+        ),
       ).rejects.toThrow("Not authorized to view these notifications.")
     })
 
@@ -422,7 +446,9 @@ describe("user resolvers", () => {
       const result = await notifications(
         { id: "u1" },
         null,
-        { userInfo: { id: "u1", admin: false, userId: "u1" } },
+        {
+          userInfo: { id: "u1", admin: false, userId: "u1" },
+        } as GraphQLContext,
       )
       expect(result.length).toBe(1)
       expect(result[0].id).toBe("event-1")
@@ -434,7 +460,9 @@ describe("user resolvers", () => {
         notifications(
           { id: "u1" },
           null,
-          { userInfo: { id: "u2", admin: false, userId: "u2" } },
+          {
+            userInfo: { id: "u2", admin: false, userId: "u2" },
+          } as GraphQLContext,
         ),
       ).rejects.toThrow("Not authorized to view these notifications.")
     })

package/src/graphql/resolvers/brainInitiative.ts

@@ -1,4 +1,4 @@
-import { redis } from "../../libs/redis"
+import { getRedis } from "../../libs/redis"
 import type { DatasetOrSnapshot } from "../../utils/datasetOrSnapshot"
 import { latestSnapshot } from "./snapshots"
 import { description } from "../../datalad/description"
@@ -6,6 +6,7 @@ import Metadata from "../../models/metadata"
 import CacheItem, { CacheType } from "../../cache/item"
 import * as Sentry from "@sentry/node"
 import fundedAwards from "../../data/funded_awards.json"
+import type { GraphQLContext } from "../builder"
 
 const brainInitiativeMatch = new RegExp("brain.initiative", "i")
 
@@ -19,10 +20,10 @@ const brainInitiativeGrants = fundedAwards.map((award) =>
 export const brainInitiative = async (
   dataset: DatasetOrSnapshot,
   _,
-  context,
+  context: GraphQLContext,
 ): Promise<boolean> => {
   const cache = new CacheItem(
-    redis,
+    getRedis(),
     CacheType.brainInitiative,
     [dataset.id],
     86400,

package/src/graphql/resolvers/cache.ts

@@ -1,25 +1,26 @@
-import { redis } from "../../libs/redis.js"
+import { getRedis } from "../../libs/redis.js"
 import { clearDatasetTrees } from "../../cache/tree"
+import type { GraphQLContext } from "../builder"
 
 /**
  * Clear all cache entries for a given datasetId
  */
 export async function cacheClear(
-  obj: Record<string, unknown>,
+  obj: unknown,
   { datasetId }: { datasetId: string },
-  { userInfo }: { userInfo: { admin: boolean } },
+  { userInfo }: GraphQLContext,
 ): Promise<boolean> {
   // Check for admin and validate datasetId argument
   if (userInfo?.admin && datasetId.length == 8 && datasetId.startsWith("ds")) {
     try {
       // Clear tree cache entries via the dataset-to-trees index
-      await clearDatasetTrees(redis, datasetId)
+      await clearDatasetTrees(getRedis(), datasetId)
 
       // Also clear non-tree cache keys (descriptions, snapshots, etc.)
-      const stream = redis.scanStream({
+      const stream = getRedis().scanStream({
         match: `*${datasetId}*`,
       })
-      const pipeline = redis.pipeline()
+      const pipeline = getRedis().pipeline()
       for await (const keys of stream) {
         for (const key of keys) {
           pipeline.del(key)

package/src/graphql/resolvers/comment.ts

@@ -1,21 +1,30 @@
 import Comment from "../../models/comment"
+import type { CommentDocument } from "../../models/comment"
 import notifications from "../../libs/notifications"
 import { user } from "./user.js"
 import { checkAdmin } from "../permissions"
+import type { GraphQLContext } from "../builder"
 
-export const comment = (obj, { id }) => {
+export const comment = (
+  obj: unknown,
+  { id }: { id: string },
+): Promise<CommentDocument | null> => {
   return Comment.findOne({ _id: id }).exec()
 }
 
-export const datasetComments = (obj) => {
+export const datasetComments = (
+  obj: { id: string },
+): Promise<CommentDocument[]> => {
   return Comment.find({ datasetId: obj.id }).exec()
 }
 
-export const userComments = (obj) => {
+export const userComments = (
+  obj: { id: string },
+): Promise<CommentDocument[]> => {
   return Comment.find({ "user._id": obj.id }).exec()
 }
 
-const replies = (obj) => {
+const replies = (obj: CommentDocument): Promise<CommentDocument[]> => {
   return Comment.find({ parentId: obj._id }).exec()
 }
 
@@ -31,7 +40,7 @@ export const flatten = (arr) => [].concat(...arr)
  * @param {import('../../models/comment').CommentDocument} obj
  * @returns {Promise<import('../../models/comment').CommentDocument[]>}
  */
-const allNestedReplies = async (obj) => {
+const allNestedReplies = async (obj: CommentDocument) => {
   const replies = await Comment.find({ parentId: obj._id }).exec()
   if (!replies.length) {
     return replies
@@ -45,9 +54,13 @@ const allNestedReplies = async (obj) => {
  * Insert new comment and return the comment _id for replies to reference
  */
 export const addComment = (
-  obj,
-  { datasetId, parentId, comment: text },
-  { user },
+  obj: unknown,
+  { datasetId, parentId, comment: text }: {
+    datasetId: string
+    parentId?: string
+    comment: string
+  },
+  { user }: GraphQLContext,
 ) => {
   if (!user) {
     return Promise.reject(
@@ -62,18 +75,18 @@ export const addComment = (
   })
   return newComment.save().then((commentInsert) => {
     notifications.commentCreated(commentInsert)
-    return commentInsert._id
+    return commentInsert._id.toString()
   })
 }
 
 export const editComment = async (
-  obj,
-  { commentId, comment: text },
-  { user },
+  obj: unknown,
+  { commentId, comment: text }: { commentId: string; comment: string },
+  { user }: GraphQLContext,
 ) => {
   const existingComment = await Comment.findById(commentId).exec()
   // You may only edit your own comments
-  if (existingComment.user._id === user) {
+  if (existingComment.user._id.toString() === user) {
     existingComment.text = text
     return existingComment.save().then(() => true)
   } else {
@@ -82,9 +95,12 @@ export const editComment = async (
 }
 
 export const deleteComment = async (
-  obj,
-  { commentId, deleteChildren = true },
-  { user, userInfo },
+  obj: unknown,
+  { commentId, deleteChildren = true }: {
+    commentId: string
+    deleteChildren?: boolean
+  },
+  { user, userInfo }: GraphQLContext,
 ) => {
   await checkAdmin(user, userInfo)
 
@@ -93,7 +109,7 @@ export const deleteComment = async (
   if (deleteChildren) {
     targetComments.push(...(await allNestedReplies(existingComment)))
   }
-  const deletedCommentIds = targetComments.map((c) => c._id)
+  const deletedCommentIds = targetComments.map((c) => c._id.toString())
   return Comment.deleteMany({
     _id: {
       $in: deletedCommentIds,
@@ -103,9 +119,9 @@ export const deleteComment = async (
 
 //"5c9bf7e3088cea6fa775c42a"
 const CommentFields = {
-  parent: (obj) => comment(obj, { id: obj.parentId }),
+  parent: (obj: CommentDocument) => comment(obj, { id: obj.parentId }),
   replies,
-  user: (obj) => user(obj, { id: obj.user._id }),
+  user: (obj: CommentDocument) => user(obj, { id: obj.user._id.toString() }),
 }
 
 export default CommentFields

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

@@ -1,11 +1,12 @@
 import * as Sentry from "@sentry/node"
-import { elasticClient } from "../../elasticsearch/elastic-client"
+import { getElasticClient } from "../../elasticsearch/elastic-client"
 import { dataset } from "./dataset"
 import Star from "../../models/stars"
 import Subscription from "../../models/subscription"
 import Permission from "../../models/permission"
 import { hashObject } from "../../libs/authentication/crypto"
 import { buildElasticQuery } from "./build-search-query"
+import type { GraphQLContext } from "../builder"
 
 const elasticIndex = "datasets"
 
@@ -16,7 +17,7 @@ const elasticIndex = "datasets"
  * @returns {Promise}
  */
 export const removeDatasetSearchDocument = (id) =>
-  elasticClient.delete({ id, index: elasticIndex })
+  getElasticClient().delete({ id, index: elasticIndex })
 
 /**
  * Accepts an array of fields representing the sort order for the search
@@ -56,7 +57,7 @@ export const elasticRelayConnection = (
         const node = childResolvers.dataset(
           null,
           { id: hit._source.id },
-          { user, userInfo },
+          { user, userInfo } as GraphQLContext,
         )
         return { id: hit._source.id, node }
       }),
@@ -100,7 +101,7 @@ export const datasetSearchConnection = async (
       // Don't include search_after if parsing fails
     }
   }
-  await elasticClient.search({
+  await getElasticClient().search({
     index: elasticIndex,
     size: first,
     q: `${q} AND public:true`,
@@ -225,7 +226,7 @@ export const advancedDatasetSearchConnection = async (
     after,
     first = 25,
   },
-  { user, userInfo },
+  { user, userInfo }: GraphQLContext,
 ) => {
   // Build the ES query from structured input
   const { query: esQuery, isEmpty } = buildElasticQuery(searchInput)
@@ -269,7 +270,7 @@ export const advancedDatasetSearchConnection = async (
     search_after,
   }
   // Run the query
-  const result = await elasticClient.search(requestBody)
+  const result = await getElasticClient().search(requestBody)
   // Extend with relay connection pagination
   return elasticRelayConnection(
     result,

package/src/graphql/resolvers/dataset.ts

@@ -1,5 +1,6 @@
 import * as datalad from "../../datalad/dataset"
 import { removeDatasetSearchDocument } from "./dataset-search"
+import { snapshotCreationComparison } from "../../utils/snapshots"
 import { latestSnapshot, snapshots } from "./snapshots"
 import { description } from "./description"
 import {
@@ -23,15 +24,24 @@ import { brainInitiative } from "./brainInitiative"
 import { derivatives } from "./derivatives"
 import { promiseTimeout } from "../../utils/promiseTimeout"
 import { datasetEvents } from "./datasetEvents"
-import semver from "semver"
 import { getDraftInfo } from "../../datalad/draft"
+import type { GraphQLContext } from "../builder"
+import type { DatasetDocument } from "../../models/dataset"
 
-export const dataset = async (obj, { id }, { user, userInfo }) => {
+export const dataset = async (
+  obj: unknown,
+  { id }: { id: string },
+  { user, userInfo }: GraphQLContext,
+) => {
   await checkDatasetRead(id, user, userInfo)
   return promiseTimeout(datalad.getDataset(id), 30000)
 }
 
-export const datasets = (parent, args, { user, userInfo }) => {
+export const datasets = (
+  parent: unknown,
+  args: Record<string, unknown>,
+  { user, userInfo }: GraphQLContext,
+) => {
   if (user) {
     return datalad.getDatasets({
       ...args,
@@ -43,22 +53,11 @@ export const datasets = (parent, args, { user, userInfo }) => {
   }
 }
 
-export const snapshotCreationComparison = (
-  { created: a, tag: a_tag },
-  { created: b, tag: b_tag },
-) => {
-  if (semver.valid(a_tag) && semver.valid(b_tag)) {
-    return semver.compare(a_tag, b_tag)
-  } else {
-    return new Date(a).getTime() - new Date(b).getTime()
-  }
-}
-
 /**
  * Find the canonical name for a dataset from snapshots and drafts
  * @param {object} obj Dataset object (at least {id: "datasetId"})
  */
-export const datasetName = (obj) => {
+export const datasetName = (obj: { id: string; revision?: string }) => {
   return snapshots(obj).then((results) => {
     if (results && results.length) {
       // Return the latest snapshot name
@@ -83,7 +82,7 @@ export const datasetName = (obj) => {
  * Resolve the best dataset name and cache in mongodb
  * @param {string} datasetId
  */
-export const updateDatasetName = (datasetId) =>
+export const updateDatasetName = (datasetId: string) =>
   datasetName({ id: datasetId }).then((name) =>
     DatasetModel.updateOne({ id: datasetId }, { $set: { name } }).exec()
   )
@@ -92,9 +91,12 @@ export const updateDatasetName = (datasetId) =>
  * Create an empty dataset (new repo, new accession number)
  */
 export const createDataset = (
-  obj,
-  { affirmedDefaced, affirmedConsent },
-  { user, userInfo },
+  obj: unknown,
+  { affirmedDefaced, affirmedConsent }: {
+    affirmedDefaced: boolean
+    affirmedConsent: boolean
+  },
+  { user, userInfo }: GraphQLContext,
 ) => {
   // Check for a valid login
   if (user) {
@@ -117,9 +119,9 @@ export const createDataset = (
  * Delete an existing dataset, as well as all snapshots
  */
 export const deleteDataset = async (
-  obj,
-  { id, reason, redirect },
-  { user, userInfo },
+  obj: unknown,
+  { id, reason, redirect }: { id: string; reason: string; redirect: string },
+  { user, userInfo }: GraphQLContext,
 ) => {
   await checkDatasetWrite(id, user, userInfo)
   const deleted = await datalad.deleteDataset(id, userInfo)
@@ -144,9 +146,9 @@ export const deleteDataset = async (
  * Delete files from a draft
  */
 export const deleteFiles = async (
-  obj,
-  { datasetId, files },
-  { user, userInfo },
+  obj: unknown,
+  { datasetId, files }: { datasetId: string; files: { path: string }[] },
+  { user, userInfo }: GraphQLContext,
 ) => {
   try {
     await checkDatasetWrite(datasetId, user, userInfo)
@@ -158,9 +160,15 @@ export const deleteFiles = async (
 }
 
 export const removeAnnexObject = async (
-  obj,
-  { datasetId, snapshot, path, filename, annexKey },
-  { user, userInfo },
+  obj: unknown,
+  { datasetId, snapshot, path, filename, annexKey }: {
+    datasetId: string
+    snapshot: string
+    path: string
+    filename: string
+    annexKey: string
+  },
+  { user, userInfo }: GraphQLContext,
 ) => {
   try {
     await checkDatasetAdmin(datasetId, user, userInfo)
@@ -179,9 +187,14 @@ export const removeAnnexObject = async (
 }
 
 export const flagAnnexObject = async (
-  obj,
-  { datasetId, snapshot, filepath, annexKey },
-  { user, userInfo },
+  obj: unknown,
+  { datasetId, snapshot, filepath, annexKey }: {
+    datasetId: string
+    snapshot: string
+    filepath: string
+    annexKey: string
+  },
+  { user, userInfo }: GraphQLContext,
 ) => {
   try {
     await checkDatasetWrite(datasetId, user, userInfo)
@@ -202,19 +215,21 @@ export const flagAnnexObject = async (
  * Update the dataset Public status
  */
 export const updatePublic = (
-  obj,
-  { datasetId, publicFlag },
-  { user, userInfo },
+  obj: unknown,
+  { datasetId, publicFlag }: { datasetId: string; publicFlag: boolean },
+  { user, userInfo }: GraphQLContext,
 ) => {
   return checkDatasetWrite(datasetId, user, userInfo).then(() => {
-    return datalad.updatePublic(datasetId, publicFlag, user)
+    return datalad.updatePublic(datasetId, publicFlag, userInfo)
   })
 }
 
 /**
  * Get analytics for a dataset or snapshot
  */
-export const analytics = async (obj) => {
+export const analytics = async (
+  obj: { id?: string; dataset?: () => Promise<{ id: string }>; tag?: string },
+) => {
   // if the dataset field exists, the request is from a snapshot, and
   // we resolve the datasetId from the dataset snapshot field of context.
   // otherwise, just use the id field because the object is a dataset
@@ -228,7 +243,10 @@ export const analytics = async (obj) => {
 /**
  * Track analytic of type 'view' or 'download' for a dataset / snapshot
  */
-export const trackAnalytics = (obj, { datasetId, tag, type }) => {
+export const trackAnalytics = (
+  obj: unknown,
+  { datasetId, tag, type }: { datasetId: string; tag: string; type: string },
+) => {
   try {
     dataladAnalytics.trackAnalytics(datasetId, tag, type)
     return true
@@ -240,7 +258,9 @@ export const trackAnalytics = (obj, { datasetId, tag, type }) => {
 /**
  * Get the star count for the dataset
  */
-export const stars = async (obj) => {
+export const stars = async (
+  obj: { id?: string; dataset?: () => Promise<{ id: string }> },
+) => {
   const datasetId = obj && obj.dataset ? (await obj.dataset()).id : obj.id
   return datalad.getStars(datasetId)
 }
@@ -248,7 +268,9 @@ export const stars = async (obj) => {
 /**
  * Get the follower count for the dataset
  */
-export const followers = async (obj) => {
+export const followers = async (
+  obj: { id?: string; dataset?: () => Promise<{ id: string }> },
+) => {
   const datasetId = obj && obj.dataset ? (await obj.dataset()).id : obj.id
   return datalad.getFollowers(datasetId)
 }
@@ -258,7 +280,11 @@ export const followers = async (obj) => {
  *
  * Returns null for anonymous users
  */
-export const following = (obj, _, { user }) =>
+export const following = (
+  obj: { id: string },
+  _: unknown,
+  { user }: { user: string },
+) =>
   user
     ? datalad.getUserFollowed(obj.id, user).then((res) => (res ? true : false))
     : null
@@ -268,19 +294,24 @@ export const following = (obj, _, { user }) =>
  *
  * Returns null for anonymous users
  */
-export const starred = (obj, _, { user }) =>
+export const starred = (
+  obj: { id: string },
+  _: unknown,
+  { user }: { user: string },
+) =>
   user
     ? datalad.getUserStarred(obj.id, user).then((res) => (res ? true : false))
     : null
 
-const worker = (obj) => getDatasetWorker(obj.id)
+const worker = (obj: { id: string }) => getDatasetWorker(obj.id)
 
 /**
  * Dataset object
  */
 const Dataset = {
-  uploader: (ds, _, context) => user(ds, { id: ds.uploader }, context),
-  draft: async (obj) => {
+  uploader: (ds: DatasetDocument, _: unknown, context: GraphQLContext) =>
+    user(ds, { id: ds.uploader }, context as never),
+  draft: async (obj: DatasetDocument) => {
     const draftHead = await getDraftInfo(obj.id)
     return {
       id: obj.id,
@@ -288,8 +319,9 @@ const Dataset = {
       modified: draftHead.modified,
     }
   },
-  snapshots,
-  latestSnapshot,
+  // Wrapper functions defer access to break the resolvers/dataset ↔ resolvers/snapshots cycle
+  snapshots: (obj) => snapshots(obj),
+  latestSnapshot: (obj, args, context) => latestSnapshot(obj, args, context),
   analytics,
   stars,
   followers,

package/src/graphql/resolvers/datasetEvents.ts

@@ -1,4 +1,5 @@
 import DatasetEvent from "../../models/datasetEvents"
+import type { GraphQLContext } from "../builder"
 import { toDbStatus, toGraphqlStatus } from "./response-status"
 import type { DbStatus, GraphqlStatus } from "./response-status"
 import User from "../../models/user"
@@ -35,9 +36,9 @@ export type EnrichedDatasetEvent =
  * Get all events for a dataset
  */
 export async function datasetEvents(
-  obj,
-  _,
-  { userInfo, user },
+  obj: { id: string },
+  _: unknown,
+  { userInfo, user }: GraphQLContext,
 ): Promise<EnrichedDatasetEvent[]> {
   const allEvents: DatasetEventDocument[] = await DatasetEvent.find({
     datasetId: obj.id,
@@ -106,9 +107,9 @@ export const DatasetEventDescriptionTypeResolvers = {
  * Create a 'contributor request' event
  */
 export async function createContributorRequestEvent(
-  obj,
-  { datasetId },
-  { user },
+  obj: unknown,
+  { datasetId }: { datasetId: string },
+  { user }: GraphQLContext,
 ) {
   if (!user) {
     throw new Error("Authentication required to request contributor status.")
@@ -149,9 +150,9 @@ export async function createContributorRequestEvent(
  * Create or update an admin note event
  */
 export async function saveAdminNote(
-  obj,
-  { id, datasetId, note },
-  { user, userInfo },
+  obj: unknown,
+  { id, datasetId, note }: { id?: string; datasetId: string; note: string },
+  { user, userInfo }: GraphQLContext,
 ) {
   if (!userInfo?.admin) throw new Error("Not authorized")
 
@@ -198,10 +199,7 @@ export async function processContributorRequest(
     resolutionStatus: "ACCEPTED" | "DENIED"
     reason?: string
   },
-  { user: currentUserId, userInfo }: {
-    user: string
-    userInfo: { admin: boolean }
-  },
+  { user: currentUserId, userInfo }: GraphQLContext,
 ) {
   if (!currentUserId) {
     throw new Error("Authentication required to process contributor requests.")
@@ -299,7 +297,11 @@ export async function processContributorRequest(
 /**
  * Update a user's notification status
  */
-export async function updateEventStatus(obj, { eventId, status }, { user }) {
+export async function updateEventStatus(
+  obj: unknown,
+  { eventId, status }: { eventId: string; status: string },
+  { user }: GraphQLContext,
+) {
   if (!user) throw new Error("Authentication required.")
   return await UserNotificationStatus.findOneAndUpdate(
     { userId: user, datasetEventId: eventId },
@@ -328,7 +330,7 @@ export async function createContributorCitationEvent(
       familyName?: string
     }
   },
-  { user }: { user: string },
+  { user }: GraphQLContext,
 ) {
   if (!user) throw new Error("Authentication required.")
 
@@ -404,7 +406,7 @@ export async function processContributorCitation(
     eventId: string
     status: "ACCEPTED" | "DENIED"
   },
-  { user, userInfo }: { user: string; userInfo: { admin?: boolean } },
+  { user, userInfo }: GraphQLContext,
 ) {
   if (!user) throw new Error("Authentication required.")