@openneuro/server 5.0.0 → 5.1.0

package/src/graphql/resolvers/draft.ts

@@ -10,9 +10,16 @@ import { filterRemovedAnnexObjects } from "../utils/file.js"
 import { validation } from "./validation"
 import FileCheck from "../../models/fileCheck"
 import { contributors } from "../../datalad/contributors"
+import type { GraphQLContext } from "../builder"
+
+export type DraftShape = { id: string; revision?: string; modified?: Date }
 
 // A draft must have a dataset parent
-export const draftFiles = async (dataset, args, { userInfo }) => {
+export const draftFiles = async (
+  dataset: DraftShape,
+  args: { tree?: string | null; recursive?: boolean | null },
+  { userInfo }: Pick<GraphQLContext, "userInfo">,
+) => {
   const hexsha = await getDraftRevision(dataset.id)
   const treeish = args.tree || hexsha
   const files = args.recursive
@@ -32,14 +39,18 @@ const draftSize = async (dataset, args, { userInfo }) => {
 /**
  * Mutation to move the draft HEAD reference forward or backward
  */
-export const revalidate = async (obj, { datasetId }, { user, userInfo }) => {
+export const revalidate = async (
+  obj: unknown,
+  { datasetId }: { datasetId: string },
+  { user, userInfo }: GraphQLContext,
+) => {
   await checkDatasetWrite(datasetId, user, userInfo)
 }
 
 /**
  * Resolve any issues with files recorded for the current commit
  */
-export const fileCheck = async (dataset) => {
+export const fileCheck = async (dataset: DraftShape) => {
   const hexsha = await getDraftRevision(dataset.id)
   // For drafts, obtain the local check results
   const checks = await FileCheck.findOne({

package/src/graphql/resolvers/fileCheck.ts

@@ -1,14 +1,15 @@
 import config from "../../config"
 import { generateDataladCookie } from "../../libs/authentication/jwt"
 import { getDatasetWorker } from "../../libs/datalad-service"
-import { redlock } from "../../libs/redis"
+import { getRedlock } from "../../libs/redis"
 import FileCheck from "../../models/fileCheck"
 import { checkDatasetAdmin, checkDatasetWrite } from "../permissions"
+import type { GraphQLContext } from "../builder"
 
 export const updateFileCheck = async (
   obj,
   { datasetId, hexsha, refs, remote, annexFsck },
-  { user, userInfo },
+  { user, userInfo }: GraphQLContext,
 ) => {
   await checkDatasetAdmin(datasetId, user, userInfo)
   return await FileCheck.findOneAndUpdate(
@@ -28,7 +29,7 @@ export const fsckUrl = (datasetId) => {
   }/datasets/${datasetId}/fsck`
 }
 
-export const fsckDataset = async (_, { datasetId }, { user, userInfo }) => {
+export const fsckDataset = async (_, { datasetId }, { user, userInfo }: GraphQLContext) => {
   // Anonymous users can't trigger fsck
   try {
     await checkDatasetWrite(datasetId, user, userInfo)
@@ -37,7 +38,7 @@ export const fsckDataset = async (_, { datasetId }, { user, userInfo }) => {
   }
   try {
     // Lock for 30 minutes to avoid stacking fsck requests
-    await redlock.lock(`openneuro:fsck-local-lock:${datasetId}`, 1800000)
+    await getRedlock().lock(`openneuro:fsck-local-lock:${datasetId}`, 1800000)
     const response = await fetch(fsckUrl(datasetId), {
       method: "POST",
       body: JSON.stringify({}),

package/src/graphql/resolvers/flaggedFiles.ts

@@ -1,10 +1,11 @@
 import BadAnnexObject from "../../models/badAnnexObject"
 import { checkAdmin } from "../permissions"
+import type { GraphQLContext } from "../builder"
 
 export const flaggedFiles = async (
   obj,
   { flagged = true, deleted = false },
-  { user, userInfo },
+  { user, userInfo }: GraphQLContext,
 ) => {
   await checkAdmin(user, userInfo)
   return BadAnnexObject.find({ flagged, removed: deleted })

package/src/graphql/resolvers/follow.ts

@@ -1,6 +1,7 @@
 import Subscription from "../../models/subscription"
+import type { GraphQLContext } from "../builder"
 
-export const followDataset = async (obj, { datasetId }, { user }) => {
+export const followDataset = async (obj, { datasetId }, { user }: GraphQLContext) => {
   const following = await Subscription.findOne({
     datasetId,
     userId: user,

package/src/graphql/resolvers/git.ts

@@ -1,6 +1,7 @@
 import { checkDatasetRead, checkDatasetWrite } from "../permissions.js"
 import { generateRepoToken } from "../../libs/authentication/jwt"
 import { getDatasetEndpoint } from "../../libs/datalad-service.js"
+import type { GraphQLContext } from "../builder"
 
 /**
  * Generate a short lived token for git operations
@@ -14,7 +15,7 @@ import { getDatasetEndpoint } from "../../libs/datalad-service.js"
 export async function prepareRepoAccess(
   _: Record<string, unknown>,
   { datasetId }: { datasetId: string },
-  { user, userInfo }: { user: string; userInfo: Record<string, unknown> },
+  { user, userInfo }: GraphQLContext,
 ): Promise<{ token: string; endpoint: number }> {
   try {
     await checkDatasetWrite(datasetId, user, userInfo)

package/src/graphql/resolvers/gitEvents.ts

@@ -1,5 +1,6 @@
 import { createEvent } from "../../libs/events"
 import { checkDatasetWrite } from "../permissions"
+import type { GraphQLContext } from "../builder"
 
 /**
  * Create a git event
@@ -7,7 +8,7 @@ import { checkDatasetWrite } from "../permissions"
 export const createGitEvent = async (
   obj,
   { datasetId, commit, reference },
-  { user, userInfo },
+  { user, userInfo }: GraphQLContext,
 ) => {
   await checkDatasetWrite(datasetId, user, userInfo)
   const event = await createEvent(

package/src/graphql/resolvers/history.ts

@@ -1,6 +1,8 @@
+import type { FlattenMaps } from "mongoose"
 import { getDatasetWorker } from "../../libs/datalad-service"
+import type { DatasetDocument } from "../../models/dataset"
 
-export const history = async (obj) => {
+export const history = async (obj: FlattenMaps<DatasetDocument>) => {
   const datasetId = obj.id
   const historyUrl = `http://${
     getDatasetWorker(

package/src/graphql/resolvers/holdDeletion.ts

@@ -5,7 +5,7 @@ import Dataset from "../../models/dataset"
  * Requires site admin access.
  */
 export async function holdDeletion(
-  _obj: Record<string, unknown>,
+  _obj: unknown,
   { datasetId, hold }: { datasetId: string; hold: boolean },
   { userInfo }: { userInfo: { admin: boolean } },
 ): Promise<boolean> {

package/src/graphql/resolvers/importRemoteDataset.ts

@@ -4,6 +4,7 @@ import { getDatasetWorker } from "../../libs/datalad-service"
 import { generateDataladCookie } from "../../libs/authentication/jwt"
 import notifications from "../../libs/notifications"
 import config from "../../config"
+import type { GraphQLContext } from "../builder"
 
 /**
  * Test if a URL is allowed to be imported
@@ -34,7 +35,7 @@ export function allowedImportUrl(raw: string): boolean {
 export async function importRemoteDataset(
   _: Record<string, unknown>,
   { datasetId, url }: { datasetId: string; url: string },
-  { user, userInfo }: { user: string; userInfo: Record<string, unknown> },
+  { user, userInfo }: GraphQLContext,
 ): Promise<string | null> {
   await checkDatasetWrite(datasetId, user, userInfo)
   if (!allowedImportUrl(url)) {
@@ -66,7 +67,7 @@ export async function finishImportRemoteDataset(
   _: Record<string, unknown>,
   { id, success, message }: { id: string; success: boolean; message: string },
   /* eslint-disable-next-line @typescript-eslint/no-unused-vars */
-  { user, userInfo }: { user: string; userInfo: Record<string, unknown> },
+  { user, userInfo }: GraphQLContext,
 ): Promise<boolean> {
   const ingest = await IngestDataset.findById(id)
   ingest.imported = success

package/src/graphql/resolvers/issues.ts

@@ -1,11 +1,12 @@
 import Issue from "../../models/issue"
 import { datasetType } from "./datasetType"
 import { revalidate } from "./validation.js"
+import type { GraphQLContext } from "../builder"
 
 /**
  * Issues resolver
  */
-export const issues = async (dataset, _, { userInfo }) => {
+export const issues = async (dataset, _, { userInfo }: GraphQLContext) => {
   return Issue.findOne({
     id: dataset.revision,
     datasetId: dataset.id,

package/src/graphql/resolvers/metadata.ts

@@ -5,6 +5,7 @@ import MetadataModel from "../../models/metadata"
 import type { MetadataDocument } from "../../models/metadata"
 import { latestSnapshot } from "./snapshots"
 import { permissions } from "./permissions"
+import type { GraphQLContext } from "../builder"
 
 /**
  * Summary resolver
@@ -14,7 +15,7 @@ import { permissions } from "./permissions"
 export const metadata = async (
   dataset,
   _,
-  context,
+  context: GraphQLContext,
 ): Promise<FlattenMaps<MetadataDocument>> => {
   const record = await MetadataModel.findOne({
     datasetId: dataset.id,
@@ -79,7 +80,7 @@ export async function publicMetadata(
   }).lean()
   const dsMetadata: FlattenMaps<MetadataDocument>[] = []
   for (const ds of datasets) {
-    dsMetadata.push(await metadata(ds, null, {}))
+    dsMetadata.push(await metadata(ds, null, {} as GraphQLContext))
   }
   return dsMetadata
 }

package/src/graphql/resolvers/permissions.ts

@@ -3,22 +3,31 @@ import type { UserDocument } from "../../models/user"
 import Permission from "../../models/permission"
 import type { PermissionDocument } from "../../models/permission"
 import { checkDatasetAdmin } from "../permissions"
+import type { GraphQLContext } from "../builder"
 import { user } from "./user"
 import { createEvent, updateEvent } from "../../libs/events"
 
-interface DatasetPermission {
+export interface DatasetPermission {
   id: string
   userPermissions: (PermissionDocument & { user: Promise<UserDocument> })[]
 }
 
-export async function permissions(ds, _, context): Promise<DatasetPermission> {
+export async function permissions(
+  ds: { id: string },
+  _: unknown,
+  context: Partial<GraphQLContext> | null,
+): Promise<DatasetPermission> {
   const permissions = await Permission.find({ datasetId: ds.id }).exec()
   return {
     id: ds.id,
     userPermissions: permissions.map(
       (userPermission) => ({
         ...userPermission.toJSON(),
-        user: user(ds, { id: userPermission.userId }, context),
+        user: user(
+          ds,
+          { id: userPermission.userId },
+          context as Partial<GraphQLContext>,
+        ),
       } as unknown as PermissionDocument & { user: Promise<UserDocument> }),
     ),
   }
@@ -71,7 +80,11 @@ async function updateUsers(datasetId: string, level: string, users) {
 /**
  * Update user permissions on a dataset
  */
-export const updatePermissions = async (obj, args, { user, userInfo }) => {
+export const updatePermissions = async (
+  obj: unknown,
+  args: { datasetId: string; userEmail: string; level: string },
+  { user, userInfo }: GraphQLContext,
+) => {
   await checkDatasetAdmin(args.datasetId, user, userInfo)
   // get all users the the email specified by permissions arg
   const users = await User.find({ email: args.userEmail })
@@ -88,7 +101,11 @@ export const updatePermissions = async (obj, args, { user, userInfo }) => {
 /**
  * ORCID variant of updatePermissions
  */
-export const updateOrcidPermissions = async (obj, args, { user, userInfo }) => {
+export const updateOrcidPermissions = async (
+  obj: unknown,
+  args: { datasetId: string; userOrcid: string; level: string },
+  { user, userInfo }: GraphQLContext,
+) => {
   await checkDatasetAdmin(args.datasetId, user, userInfo)
   // Get all users associated with the ORCID provided
   const users = await User.find({
@@ -110,7 +127,10 @@ export const updateOrcidPermissions = async (obj, args, { user, userInfo }) => {
 /**
  * Remove user permissions on a dataset
  */
-export const removePermissions = (obj, args) => {
+export const removePermissions = (
+  obj: unknown,
+  args: { datasetId: string; userId: string },
+) => {
   return Permission.deleteOne({
     datasetId: args.datasetId,
     userId: args.userId,

package/src/graphql/resolvers/publish.ts

@@ -4,8 +4,9 @@ import { updatePublic } from "../../datalad/dataset"
 import { checkDatasetWrite } from "../permissions.js"
 import { generateDataladCookie } from "../../libs/authentication/jwt"
 import { getDatasetWorker } from "../../libs/datalad-service"
+import type { GraphQLContext } from "../builder"
 
-export const publishDataset = (obj, { datasetId }, { user, userInfo }) => {
+export const publishDataset = (obj, { datasetId }, { user, userInfo }: GraphQLContext) => {
   return checkDatasetWrite(datasetId, user, userInfo).then(async () => {
     await updatePublic(datasetId, true, userInfo)
     const uri = `${getDatasetWorker(datasetId)}/datasets/${datasetId}/publish`

package/src/graphql/resolvers/readme.ts

@@ -4,13 +4,14 @@
  */
 import { setReadme } from "../../datalad/readme"
 import { checkDatasetWrite } from "../permissions"
+import type { GraphQLContext } from "../builder"
 export { readme } from "../../datalad/readme"
 import { draftFiles } from "./draft"
 
 export async function updateReadme(
   obj,
   { datasetId, value },
-  { user, userInfo },
+  { user, userInfo }: GraphQLContext,
 ) {
   await checkDatasetWrite(datasetId, user, userInfo)
   const files = await draftFiles({ id: datasetId }, { tree: "HEAD" }, {

package/src/graphql/resolvers/reexporter.ts

@@ -3,11 +3,12 @@
  */
 import { checkAdmin } from "../permissions"
 import { runReexporter } from "../../datalad/reexporter"
+import type { GraphQLContext } from "../builder"
 
 export const reexportRemotes = async (
   obj,
   { datasetId },
-  { user, userInfo },
+  { user, userInfo }: GraphQLContext,
 ) => {
   await checkAdmin(user, userInfo)
   await runReexporter(datasetId)

package/src/graphql/resolvers/relation.ts

@@ -1,11 +1,12 @@
 import Dataset from "../../models/dataset"
 import { checkDatasetAdmin } from "../permissions"
 import { DOIPattern } from "../../libs/doi/normalize"
+import type { GraphQLContext } from "../builder"
 
 export const createRelation = async (
   obj,
   { datasetId, doi, relation, kind, description },
-  { user, userInfo },
+  { user, userInfo }: GraphQLContext,
 ) => {
   await checkDatasetAdmin(datasetId, user, userInfo)
   // Validate the right DOI format
@@ -27,7 +28,7 @@ export const createRelation = async (
 export const deleteRelation = async (
   obj,
   { datasetId, doi },
-  { user, userInfo },
+  { user, userInfo }: GraphQLContext,
 ) => {
   await checkDatasetAdmin(datasetId, user, userInfo)
   return await Dataset.findOneAndUpdate(

package/src/graphql/resolvers/reset.ts

@@ -1,5 +1,6 @@
 import { checkDatasetWrite } from "../permissions"
 import { resetDraft as resetDraftTask } from "../../datalad/draft"
+import type { GraphQLContext } from "../builder"
 
 /**
  * Mutation to move the draft HEAD reference forward or backward
@@ -7,7 +8,7 @@ import { resetDraft as resetDraftTask } from "../../datalad/draft"
 export const resetDraft = async (
   obj,
   { datasetId, ref },
-  { user, userInfo },
+  { user, userInfo }: GraphQLContext,
 ) => {
   await checkDatasetWrite(datasetId, user, userInfo)
   try {

package/src/graphql/resolvers/reviewer.ts

@@ -2,6 +2,7 @@ import config from "../../config"
 import Reviewer from "../../models/reviewer"
 import { checkDatasetAdmin } from "../permissions.js"
 import { generateReviewerToken } from "../../libs/authentication/jwt"
+import type { GraphQLContext } from "../builder"
 
 /**
  * Create an anonymous read-only access key
@@ -12,7 +13,11 @@ import { generateReviewerToken } from "../../libs/authentication/jwt"
  * @param {string} context.user User id
  * @param {object} context.userInfo Decoded userInfo from token
  */
-export async function createReviewer(obj, { datasetId }, { user, userInfo }) {
+export async function createReviewer(
+  obj: unknown,
+  { datasetId }: { datasetId: string },
+  { user, userInfo }: GraphQLContext,
+) {
   await checkDatasetAdmin(datasetId, user, userInfo)
   const reviewer = new Reviewer({ datasetId, creator: user })
   await reviewer.save()
@@ -26,9 +31,9 @@ export async function createReviewer(obj, { datasetId }, { user, userInfo }) {
 }
 
 export async function deleteReviewer(
-  obj,
-  { datasetId, id },
-  { user, userInfo },
+  obj: unknown,
+  { datasetId, id }: { datasetId: string; id: string },
+  { user, userInfo }: GraphQLContext,
 ) {
   await checkDatasetAdmin(datasetId, user, userInfo)
   return Reviewer.findOneAndDelete({ id }).lean().exec()
@@ -37,7 +42,10 @@ export async function deleteReviewer(
 /**
  * Resolver for dataset reviewers
  */
-/* eslint-disable-next-line @typescript-eslint/no-unused-vars */
-export function reviewers(obj, _, { user, userInfo }) {
+export function reviewers(
+  obj: { id: string },
+  _: unknown,
+  _ctx: GraphQLContext,
+) {
   return Reviewer.find({ datasetId: obj.id }).lean().exec()
 }

package/src/graphql/resolvers/snapshots.ts

@@ -1,5 +1,6 @@
 import * as datalad from "../../datalad/snapshots"
-import { analytics, dataset, snapshotCreationComparison } from "./dataset.js"
+import { analytics, dataset } from "./dataset.js"
+import { snapshotCreationComparison } from "../../utils/snapshots"
 import { onBrainlife } from "./brainlife"
 import { checkDatasetRead, checkDatasetWrite } from "../permissions"
 import { readme } from "./readme.js"
@@ -11,23 +12,49 @@ import Summary from "../../models/summary"
 import DatasetModel from "../../models/dataset"
 import { filterRemovedAnnexObjects } from "../utils/file"
 import DeprecatedSnapshot from "../../models/deprecatedSnapshot"
-import { redis } from "../../libs/redis"
+import { getRedis } from "../../libs/redis"
 import CacheItem, { CacheType } from "../../cache/item"
 import { normalizeDOI } from "../../libs/doi/normalize"
 import { snapshotValidation } from "./validation"
 import { advancedDatasetSearchConnection } from "./dataset-search"
 import { contributors } from "../../datalad/contributors"
 import { getDraftInfo } from "../../datalad/draft"
+import type { GraphQLContext } from "../builder"
+
+/**
+ * Shape returned by the snapshot() resolver, combining plain data
+ * from the HTTP API with lazy-loaded thunk fields.
+ */
+export interface SnapshotShape {
+  id: string
+  datasetId: string
+  tag: string
+  created?: Date
+  hexsha?: string
+  dataset: () => Promise<unknown>
+  description: () => Promise<unknown>
+  readme: () => Promise<unknown>
+  summary: () => Promise<unknown>
+  files: (args: {
+    tree?: string | null
+    recursive?: boolean | null
+  }) => Promise<unknown>
+  size: () => Promise<unknown>
+  deprecated: () => Promise<unknown>
+  related: () => Promise<unknown>
+  onBrainlife: () => Promise<boolean>
+}
 
 export const snapshots = (obj) => {
   return datalad.getSnapshots(obj.id)
 }
 
-export const snapshot = (obj, { datasetId, tag }, context) => {
+export const snapshot = (obj, { datasetId, tag }, context: GraphQLContext) => {
   return checkDatasetRead(datasetId, context.user, context.userInfo).then(
     () => {
       return datalad.getSnapshot(datasetId, tag).then((snapshot) => ({
         ...snapshot,
+        created: snapshot.created ? new Date(snapshot.created) : undefined,
         datasetId,
         dataset: () => dataset(snapshot, { id: datasetId }, context),
         description: () => description(snapshot),
@@ -100,7 +127,7 @@ export const matchKnownObjects = (desc) => {
 export const deprecateSnapshot = async (
   obj,
   { datasetId, tag, reason },
-  { user, userInfo },
+  { user, userInfo }: GraphQLContext,
 ) => {
   const id = `${datasetId}:${tag}`
   await checkDatasetWrite(datasetId, user, userInfo)
@@ -129,7 +156,7 @@ export const deprecateSnapshot = async (
 export const undoDeprecateSnapshot = async (
   obj,
   { datasetId, tag },
-  { user, userInfo },
+  { user, userInfo }: GraphQLContext,
 ) => {
   const id = `${datasetId}:${tag}`
   await checkDatasetWrite(datasetId, user, userInfo)
@@ -148,7 +175,7 @@ const brainInitiativeQuery = {
 export const participantCount = (obj, { modality }) => {
   const cacheKey = modality || "all"
   const cache = new CacheItem(
-    redis,
+    getRedis(),
     CacheType.participantCount,
     [cacheKey],
     86400,
@@ -172,11 +199,12 @@ export const participantCount = (obj, { modality }) => {
           datasetStatus: "",
           after,
           first: 100,
-        }, { user: null, userInfo: {} })
+        }, { user: null, userInfo: {} } as unknown as GraphQLContext)
         nihDatasets.push(...results.edges.map((edge) => edge.id))
         if (!results.pageInfo.hasNextPage) {
           break
         } else {
+          // eslint-disable-next-line no-useless-assignment
           after = results.pageInfo.endCursor
         }
       }
@@ -261,7 +289,7 @@ export const filterLatestSnapshot = (snapshots) => {
   }
 }
 
-export const latestSnapshot = async (obj, _, context) => {
+export const latestSnapshot = async (obj, _, context: GraphQLContext) => {
   const snapshots = await datalad.getSnapshots(obj.id)
   const snapshotTag = filterLatestSnapshot(snapshots)
   if (snapshotTag) {
@@ -282,7 +310,7 @@ export const latestSnapshot = async (obj, _, context) => {
 export const createSnapshot = (
   obj,
   { datasetId, tag, changes },
-  { user, userInfo },
+  { user, userInfo }: GraphQLContext,
 ) => {
   return checkDatasetWrite(datasetId, user, userInfo).then(async () => {
     return datalad.createSnapshot(datasetId, tag, userInfo, {}, changes)
@@ -292,7 +320,11 @@ export const createSnapshot = (
 /**
  * Remove a tag from a dataset
  */
-export const deleteSnapshot = (obj, { datasetId, tag }, { user, userInfo }) => {
+export const deleteSnapshot = (
+  obj,
+  { datasetId, tag },
+  { user, userInfo }: GraphQLContext,
+) => {
   return checkDatasetWrite(datasetId, user, userInfo).then(() => {
     return datalad.deleteSnapshot(datasetId, tag)
   })

package/src/graphql/resolvers/stars.ts

@@ -1,6 +1,7 @@
 import Star from "../../models/stars"
+import type { GraphQLContext } from "../builder"
 
-export const starDataset = async (obj, { datasetId }, { user }) => {
+export const starDataset = async (obj, { datasetId }, { user }: GraphQLContext) => {
   const star = await Star.findOne({ datasetId, userId: user }).exec()
   const newStar = {
     datasetId,

package/src/graphql/resolvers/upload.ts

@@ -3,6 +3,7 @@ import { checkDatasetWrite } from "../permissions.js"
 import { generateUploadToken } from "../../libs/authentication/jwt"
 import { finishUploadRequest } from "../../datalad/upload.js"
 import { getDatasetEndpoint } from "../../libs/datalad-service.js"
+import type { GraphQLContext } from "../builder"
 
 /**
  * Track initial state for a new upload
@@ -19,7 +20,7 @@ import { getDatasetEndpoint } from "../../libs/datalad-service.js"
 export async function prepareUpload(
   obj,
   { datasetId, uploadId },
-  { user, userInfo },
+  { user, userInfo }: GraphQLContext,
 ) {
   await checkDatasetWrite(datasetId, user, userInfo)
   const upload = await Upload.findOneAndUpdate(
@@ -47,7 +48,7 @@ export async function prepareUpload(
  * @param {string} context.user User id
  * @param {object} context.userInfo Decoded userInfo from token
  */
-export async function finishUpload(obj, { uploadId }, { user, userInfo }) {
+export async function finishUpload(obj, { uploadId }, { user, userInfo }: GraphQLContext) {
   const upload = await Upload.findOne({ id: uploadId })
   const datasetId = upload.datasetId
   await checkDatasetWrite(datasetId, user, userInfo)