@openneuro/server 5.1.0 → 5.1.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openneuro/server",
-  "version": "5.1.0",
+  "version": "5.1.2",
   "description": "Core service for the OpenNeuro platform.",
   "license": "MIT",
   "main": "src/server.js",
@@ -22,7 +22,7 @@
     "@elastic/elasticsearch": "8.13.1",
     "@graphql-tools/schema": "^10.0.0",
     "@keyv/redis": "^4.5.0",
-    "@openneuro/search": "^5.1.0",
+    "@openneuro/search": "^5.1.2",
     "@pothos/core": "^4.12.0",
     "@pothos/plugin-directives": "^4.3.0",
     "@pothos/plugin-simple-objects": "^4.1.3",
@@ -72,7 +72,7 @@
     "ts-node": "10.9.2",
     "typescript": "5.6.3",
     "underscore": "^1.8.3",
-    "uuid": "14.0.0",
+    "uuid": "11.1.1",
     "xmldoc": "^1.1.0"
   },
   "devDependencies": {
@@ -95,5 +95,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "e3444f63f43cb7e9d3ecfac51d2a42cdcc4f4e60"
+  "gitHead": "bccaddf537a2950100549b992a846768c32d683e"
 }

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

@@ -23,7 +23,7 @@ describe("dataset model operations", () => {
       connect(mongod.getUri())
     })
     it("resolves to dataset id string", async () => {
-      const user = { id: "1234" }
+      const user = { id: "1234", userId: "1234", admin: false }
       const { id: dsId } = await createDataset(user.id, user, {
         affirmedDefaced: true,
         affirmedConsent: true,
@@ -32,7 +32,7 @@ describe("dataset model operations", () => {
       expect(dsId.slice(0, 2)).toBe("ds")
     })
     it("posts to the DataLad /datasets/{dsId} endpoint", async () => {
-      const user = { id: "1234" }
+      const user = { id: "1234", userId: "1234", admin: false }
       // Reset call count for request.post
       request.post.mockClear()
       const { id: dsId } = await createDataset(user.id, user, {

package/src/datalad/__tests__/snapshots.spec.ts

@@ -34,7 +34,7 @@ describe("snapshot model operations", () => {
       connect(mongod.getUri())
     })
     it("posts to the DataLad /datasets/{dsId}/snapshots/{snapshot} endpoint", async () => {
-      const user = { id: "1234" }
+      const user = { id: "1234", userId: "1234", admin: false }
       const tag = "snapshot"
       const { id: dsId } = await createDataset(user.id, user, {
         affirmedDefaced: true,

package/src/datalad/dataset.ts

@@ -28,8 +28,9 @@ import { getDatasetWorker } from "../libs/datalad-service"
 import { createEvent, updateEvent } from "../libs/events"
 import Doi from "../models/doi"
 import { hideDoi, publishDoi } from "../libs/doi/index"
+import type { UserInfo } from "../graphql/builder"
 
-export const giveUploaderPermission = (datasetId, userId) => {
+export const giveUploaderPermission = (datasetId: string, userId: string) => {
   const permission = new Permission({ datasetId, userId, level: "admin" })
   return permission.save()
 }
@@ -46,8 +47,11 @@ export const giveUploaderPermission = (datasetId, userId) => {
  */
 export const createDataset = async (
   uploader: string,
-  userInfo,
-  { affirmedDefaced, affirmedConsent },
+  userInfo: UserInfo,
+  { affirmedDefaced, affirmedConsent }: {
+    affirmedDefaced: boolean
+    affirmedConsent: boolean
+  },
 ) => {
   // Obtain an accession number
   const datasetId = await getAccessionNumber()
@@ -87,7 +91,9 @@ type DatasetWithRevision = Mongoose.FlattenMaps<DatasetDocument> & {
 /**
  * Fetch dataset document and related fields
  */
-export const getDataset = async (id): Promise<DatasetWithRevision | null> => {
+export const getDataset = async (
+  id: string,
+): Promise<DatasetWithRevision | null> => {
   const dataset = await Dataset.findOne({ id }).lean()
   return dataset && {
     ...dataset,
@@ -98,7 +104,7 @@ export const getDataset = async (id): Promise<DatasetWithRevision | null> => {
 /**
  * Delete dataset and associated documents
  */
-export const deleteDataset = async (datasetId, user) => {
+export const deleteDataset = async (datasetId: string, user: UserInfo) => {
   const event = await createEvent(
     datasetId,
     user.id,
@@ -498,7 +504,11 @@ export const flagAnnexObject = (
 /**
  * Update public state and transition DOI states accordingly.
  */
-export async function updatePublic(datasetId, publicFlag, user) {
+export async function updatePublic(
+  datasetId: string,
+  publicFlag: boolean,
+  user: UserInfo,
+): Promise<boolean> {
   const event = await createEvent(
     datasetId,
     user.id,
@@ -535,6 +545,8 @@ export async function updatePublic(datasetId, publicFlag, user) {
   } catch (err) {
     Sentry.captureException(err)
   }
+  // Return the new public state
+  return publicFlag
 }
 
 export const getDatasetAnalytics = (datasetId, _tag) => {

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

@@ -33,4 +33,15 @@ describe("GraphQL derivatives", () => {
       })
     })
   })
+  it("returns expected values for fitlins", () => {
+      expect(derivativeObject("ds000002", "fitlins")).toEqual({
+        dataladUrl: new URL(
+          "https://github.com/OpenNeuroDerivatives/ds000002-fitlins.git",
+        ),
+        local: false,
+        name: "ds000002-fitlins",
+        s3Url: new URL("s3://openneuro-derivatives/fitlins/ds000002-fitlins"),
+      })
+    })
+
 })

package/src/graphql/resolvers/dataset.ts

@@ -220,7 +220,7 @@ export const updatePublic = (
   { user, userInfo }: GraphQLContext,
 ) => {
   return checkDatasetWrite(datasetId, user, userInfo).then(() => {
-    return datalad.updatePublic(datasetId, publicFlag, user)
+    return datalad.updatePublic(datasetId, publicFlag, userInfo)
   })
 }
 

package/src/graphql/resolvers/derivatives.ts

@@ -6,7 +6,7 @@ const S3_BUCKET = "openneuro-derivatives"
 const GITHUB_ORGANIZATION = "OpenNeuroDerivatives"
 
 // Available derivatives at this time
-type GitHubDerivative = "mriqc" | "fmriprep"
+type GitHubDerivative = "mriqc" | "fmriprep" | "fitlins"
 
 /**
  * Test for a derivative on GitHub via API
@@ -90,5 +90,9 @@ export const derivatives = async (
   if (await githubDerivative(datasetId, "fmriprep")) {
     available.push(derivativeObject(datasetId, "fmriprep"))
   }
+  if (await githubDerivative(datasetId, "fitlins")) {
+    available.push(derivativeObject(datasetId, "fitlins"))
+  }
+
   return available
 }

package/src/graphql/resolvers/user.ts

@@ -25,6 +25,7 @@ export type GraphQLUserType = {
   githubSynced: Date
   links: string[]
   orcidConsent: boolean | null
+  profilePrivate: boolean
 }
 
 export async function user(
@@ -50,6 +51,7 @@ export async function user(
       githubSynced: oneWeekAgo,
       links: [],
       orcidConsent: true,
+      profilePrivate: false,
       created: oneWeekAgo,
       lastSeen: new Date(),
       updatedAt: oneWeekAgo,
@@ -232,12 +234,13 @@ export const setBlocked = (
 
 export const updateUser = async (
   obj: unknown,
-  { id, location, institution, links, orcidConsent }: {
+  { id, location, institution, links, orcidConsent, profilePrivate }: {
     id: string
     location?: string
     institution?: string
     links?: string[]
     orcidConsent?: boolean
+    profilePrivate?: boolean
   },
   { userInfo }: GraphQLContext,
 ) => {
@@ -270,6 +273,7 @@ export const updateUser = async (
     if (institution !== undefined) user.institution = institution
     if (links !== undefined) user.links = links
     if (orcidConsent !== undefined) user.orcidConsent = orcidConsent
+    if (profilePrivate !== undefined) user.profilePrivate = profilePrivate
 
     await user.save()
 

package/src/graphql/schema/mutation.ts

@@ -25,7 +25,7 @@ import {
   ValidatorInput,
 } from "./inputs"
 
-import Mutation from '../resolvers/mutation'
+import Mutation from "../resolvers/mutation"
 
 builder.mutationType({
   fields: (t) => ({
@@ -142,7 +142,8 @@ builder.mutationType({
         datasetId: t.arg.id({ required: true }),
         userId: t.arg.string({ required: true }),
       },
-      resolve: (root, args) => Mutation.removePermissions(root, args as never) as never,
+      resolve: (root, args) =>
+        Mutation.removePermissions(root, args as never) as never,
     }),
     removeUser: t.boolean({
       args: {
@@ -177,6 +178,7 @@ builder.mutationType({
         institution: t.arg.string(),
         links: t.arg.stringList(),
         orcidConsent: t.arg.boolean(),
+        profilePrivate: t.arg.boolean(),
       },
       resolve: (root, args, ctx) =>
         Mutation.updateUser(root, args as never, ctx),

package/src/graphql/schema/user.ts

@@ -47,6 +47,7 @@ UserRef.implement({
       resolve: (obj, args, ctx) => notifications(obj, args, ctx),
     }),
     orcidConsent: t.boolean({ resolve: (obj) => obj.orcidConsent }),
+    profilePrivate: t.boolean({ resolve: (obj) => obj.profilePrivate }),
   }),
 })
 

package/src/models/user.ts

@@ -45,6 +45,8 @@ export interface UserDocument extends Document {
   githubSynced: Date
   // Defaults to NULL populated from ORCID Consent Form Mutation
   orcidConsent?: boolean | null
+  // Whether the user has opted out of public profile visibility
+  profilePrivate?: boolean
   givenName?: string
   familyName?: string
 }
@@ -73,6 +75,10 @@ const userSchema = new Schema({
     type: Boolean,
     default: null,
   },
+  profilePrivate: {
+    type: Boolean,
+    default: false,
+  },
 }, { timestamps: { createdAt: false, updatedAt: true } })
 
 userSchema.index({ id: 1, provider: 1 }, { unique: true })