@openneuro/server 4.29.9 → 4.30.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openneuro/server",
-  "version": "4.29.9",
+  "version": "4.30.0",
   "description": "Core service for the OpenNeuro platform.",
   "license": "MIT",
   "main": "src/server.js",
@@ -21,7 +21,7 @@
     "@elastic/elasticsearch": "8.13.1",
     "@graphql-tools/schema": "^10.0.0",
     "@keyv/redis": "^2.7.0",
-    "@openneuro/search": "^4.29.9",
+    "@openneuro/search": "^4.30.0",
     "@sentry/node": "^8.25.0",
     "@sentry/profiling-node": "^8.25.0",
     "base64url": "^3.0.0",
@@ -43,7 +43,7 @@
     "keyv": "^4.5.3",
     "mime-types": "^2.1.19",
     "mongodb-memory-server": "^9.2.0",
-    "mongoose": "6.12.8",
+    "mongoose": "6.13.5",
     "morgan": "^1.6.1",
     "node-mailjet": "^3.3.5",
     "object-hash": "2.1.1",
@@ -85,5 +85,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "992fc9e3044c67f6d85757ecf252845cfda6e809"
+  "gitHead": "e66b349543fde2fb8a8ccba580647e6ad8f4e01b"
 }

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

@@ -14,5 +14,14 @@ describe("user resolvers", () => {
         ),
       ).rejects.toEqual(new Error("You must be a site admin to retrieve users"))
     })
+    it("throws an error for non-admins", () => {
+      expect(
+        users(
+          null,
+          { id: "0000-0000-0000-000X" },
+          { userInfo: {} },
+        ),
+      ).rejects.toEqual(new Error("You must be a site admin to retrieve users"))
+    })
   })
 })

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

@@ -0,0 +1,22 @@
+import { validationSeveritySort } from "../validation"
+
+vi.mock("../../../config.ts")
+
+describe("validation resolvers", () => {
+  describe("validationSeveritySort", () => {
+    it("sorts severity error before warning", () => {
+      const issues = [
+        { severity: "warning" },
+        { severity: "error" },
+        { severity: "error" },
+        { severity: "warning" },
+        { severity: "error" },
+      ]
+      const sortedIssues = issues.sort(validationSeveritySort)
+      expect(sortedIssues[0].severity).toBe("error")
+      expect(sortedIssues[1].severity).toBe("error")
+      expect(sortedIssues[2].severity).toBe("error")
+      expect(sortedIssues[3].severity).toBe("warning")
+    })
+  })
+})

package/src/graphql/resolvers/mutation.ts

@@ -16,7 +16,7 @@ import {
   deprecateSnapshot,
   undoDeprecateSnapshot,
 } from "./snapshots.js"
-import { removeUser, setAdmin, setBlocked } from "./user.js"
+import { removeUser, setAdmin, setBlocked, updateUser } from "./user.js"
 import { updateSummary } from "./summary"
 import { revalidate, updateValidation } from "./validation.js"
 import {
@@ -88,6 +88,7 @@ const Mutation = {
   deleteRelation,
   importRemoteDataset,
   finishImportRemoteDataset,
+  updateUser,
 }
 
 export default Mutation

package/src/graphql/resolvers/user.ts

@@ -2,9 +2,19 @@
  * User resolvers
  */
 import User from "../../models/user"
+function isValidOrcid(orcid: string): boolean {
+  return /^[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]$/.test(orcid || "")
+}
 
 export const user = (obj, { id }) => {
-  return User.findOne({ id }).exec()
+  if (isValidOrcid(id)) {
+    return User.findOne({
+      $or: [{ "orcid": id }, { "providerId": id }],
+    }).exec()
+  } else {
+    // If it's not a valid ORCID, fall back to querying by user id
+    return User.findOne({ "id": id }).exec()
+  }
 }
 
 export const users = (obj, args, { userInfo }) => {
@@ -43,6 +53,36 @@ export const setBlocked = (obj, { id, blocked }, { userInfo }) => {
   }
 }
 
+export const updateUser = async (obj, { id, location, institution, links }) => {
+  try {
+    let user // Declare user outside the if block
+
+    if (isValidOrcid(id)) {
+      user = await User.findOne({
+        $or: [{ "orcid": id }, { "providerId": id }],
+      }).exec()
+    } else {
+      user = await User.findOne({ "id": id }).exec()
+    }
+
+    if (!user) {
+      throw new Error("User not found")
+    }
+
+    // Update user fields (optional values based on provided inputs)
+    if (location !== undefined) user.location = location
+    if (institution !== undefined) user.institution = institution
+    if (links !== undefined) user.links = links
+
+    // Save the updated user
+    await user.save()
+
+    return user // Return the updated user object
+  } catch (err) {
+    throw new Error("Failed to update user: " + err.message)
+  }
+}
+
 const UserResolvers = {
   id: (obj) => obj.id,
   provider: (obj) => obj.provider,
@@ -55,6 +95,9 @@ const UserResolvers = {
   name: (obj) => obj.name,
   admin: (obj) => obj.admin,
   blocked: (obj) => obj.blocked,
+  location: (obj) => obj.location,
+  institution: (obj) => obj.institution,
+  links: (obj) => obj.links,
 }
 
 export default UserResolvers

package/src/graphql/resolvers/validation.ts

@@ -38,12 +38,21 @@ export const snapshotValidation = async (snapshot) => {
     .exec()
 }
 
+export function validationSeveritySort(a, b) {
+  return a.severity.localeCompare(b.severity)
+}
+
 /**
  * Save issues data returned by the datalad service
  *
  * Returns only a boolean if successful or not
  */
 export const updateValidation = (obj, args) => {
+  // Limit to 50k issues with errors sorted first
+  if (args.validation.issues.length > 50000) {
+    args.validation.issues.sort(validationSeveritySort)
+    args.validation.issues = args.validation.issues.slice(0, 50000)
+  }
   return Validation.updateOne(
     {
       id: args.validation.id,

package/src/graphql/schema.ts

@@ -132,6 +132,8 @@ export const typeDefs = `
     setAdmin(id: ID!, admin: Boolean!): User
     # Sets a users admin status
     setBlocked(id: ID!, blocked: Boolean!): User
+    # Mutation for updating user data
+    updateUser(id: ID!, location: String, institution: String, links: [String]): User
     # Tracks a view or download for a dataset
     trackAnalytics(datasetId: ID!, tag: String, type: AnalyticTypes): Boolean
     # Follow dataset
@@ -322,6 +324,10 @@ export const typeDefs = `
     name: String
     admin: Boolean
     blocked: Boolean
+    location: String
+    institution: String
+    github: String
+    links: [String]
   }
 
   # Which provider a user login comes from
@@ -832,5 +838,4 @@ schemaComposer.addTypeDefs(typeDefs)
 schemaComposer.addResolveMethods(resolvers)
 schemaComposer.Query.addFields(datasetSearch)
 schemaComposer.Query.addFields(advancedDatasetSearch)
-
 export default schemaComposer.buildSchema()

package/src/models/user.ts

@@ -15,6 +15,10 @@ export interface UserDocument extends Document {
   blocked: boolean
   created: Date
   lastSeen: Date
+  location: string
+  institution: string
+  github: string
+  links: string[]
 }
 
 const userSchema = new Schema({
@@ -29,10 +33,14 @@ const userSchema = new Schema({
   blocked: { type: Boolean, default: false },
   created: { type: Date, default: Date.now },
   lastSeen: { type: Date, default: Date.now },
+  location: { type: String, default: "" },
+  institution: { type: String, default: "" },
+  github: { type: String, default: "" },
+  links: { type: [String], default: [] },
 })
 
 userSchema.index({ id: 1, provider: 1 }, { unique: true })
-// Allow case insensitive email queries
+// Allow case-insensitive email queries
 userSchema.index(
   { email: 1 },
   {