Merge pull request #3890 from effigies/refactor/pothos-schema-v2

rf(graphql): Generate GraphQL schema with Pothos

Author: nellh

.pnp.cjs

@@ -23,6 +23,9 @@
     "@graphql-tools/schema": "^10.0.0",
     "@keyv/redis": "^4.5.0",
     "@openneuro/search": "^5.0.1",
+    "@pothos/core": "^4.12.0",
+    "@pothos/plugin-directives": "^4.3.0",
+    "@pothos/plugin-simple-objects": "^4.1.3",
     "@sentry/node": "^10.37.0",
     "@sentry/profiling-node": "^10.37.0",
     "base64url": "^3.0.0",
@@ -34,9 +37,9 @@
     "express": "5",
     "graphql": "16.8.1",
     "graphql-bigint": "^1.0.0",
-    "graphql-compose": "9.0.10",
     "graphql-iso-date": "^3.6.1",
     "graphql-tools": "9.0.0",
+    "graphql-type-json": "^0.3.2",
     "hash-wasm": "^4.12.0",
     "immutable": "^4.3.8",
     "ioredis": "^5.6.1",

packages/openneuro-server/package.json

@@ -0,0 +1,40 @@
+/**
+ * Script to dump the GraphQL schema to a file.
+ * This was written during the transition to Pothos-generated schema,
+ * for comparison with the hand-written schema.
+ *
+ * It is written as a test because the schema's imports are entangled
+ * with the rest of the server code, and this allows us to mock out the dependencies.
+ */
+import { vi } from "vitest"
+
+vi.mock("ioredis", () => {
+  const RedisMock = vi.fn()
+  RedisMock.prototype.on = vi.fn()
+  RedisMock.prototype.connect = vi.fn()
+  return { default: RedisMock }
+})
+vi.mock("../src/elasticsearch/elastic-client", () => ({
+  elasticClient: {},
+}))
+vi.mock("../src/config", () => ({
+  default: {
+    url: "http://localhost",
+    auth: { jwt: { secret: "test-secret-for-schema-dump" } },
+    datalad: { uri: "http://localhost" },
+    mongo: { url: "mongodb://localhost", dbName: "test" },
+    redis: {},
+  },
+}))
+
+import { writeFileSync } from "fs"
+import { dirname, join } from "path"
+import { fileURLToPath } from "url"
+import { lexicographicSortSchema, printSchema } from "graphql/index.js"
+import schema from "../src/graphql/schema"
+
+it("dumps Pothos schema to SDL", () => {
+  const sdl = printSchema(lexicographicSortSchema(schema))
+  const dir = dirname(fileURLToPath(import.meta.url))
+  writeFileSync(join(dir, "..", "schema.graphql"), sdl + "\n")
+})

packages/openneuro-server/scripts/dump-schema.test.ts

@@ -28,7 +28,6 @@ export { Express } from "express-serve-static-core"
 
 interface OpenNeuroRequestContext {
   user: string
-  isSuperUser: boolean
   userInfo: {
     id: string
     exp: string
@@ -109,7 +108,6 @@ export async function expressApolloSetup() {
         if (req.isAuthenticated()) {
           return {
             user: req.user.id,
-            isSuperUser: req.user.admin,
             userInfo: req.user,
           }
         }

packages/openneuro-server/src/app.ts

@@ -13,7 +13,7 @@ type DraftInfo = {
   hexsha: string // Duplicate of ref for backwards compatibility
   tree: string
   message: string
-  modified: Date
+  modified: string
 }
 
 export const getDraftRevision = async (datasetId): Promise<string> => {

packages/openneuro-server/src/datalad/draft.ts

@@ -3,6 +3,7 @@ import { connect } from "mongoose"
 import { deleteComment, flatten } from "../resolvers/comment"
 import { MongoMemoryServer } from "mongodb-memory-server"
 import Comment from "../../models/comment"
+import type { GraphQLContext } from "../builder"
 
 vi.mock("ioredis")
 
@@ -12,11 +13,11 @@ describe("comment resolver helpers", () => {
     const adminUser = {
       user: "1234",
       userInfo: { admin: true },
-    }
+    } as GraphQLContext
     const nonAdminUser = {
       user: "5678",
       userInfo: { admin: false },
-    }
+    } as GraphQLContext
     let mongod
     beforeAll(async () => {
       // Setup MongoDB with mongodb-memory-server

packages/openneuro-server/src/graphql/__tests__/comment.spec.ts

@@ -0,0 +1,28 @@
+import { vi } from "vitest"
+
+vi.mock("ioredis", () => {
+  const RedisMock = vi.fn()
+  RedisMock.prototype.on = vi.fn()
+  RedisMock.prototype.connect = vi.fn()
+  return { default: RedisMock }
+})
+vi.mock("../../elasticsearch/elastic-client", () => ({
+  elasticClient: {},
+}))
+vi.mock("../../config", () => ({
+  default: {
+    url: "http://localhost",
+    auth: { jwt: { secret: "test-secret-for-schema-smoke" } },
+    datalad: { uri: "http://localhost" },
+    mongo: { url: "mongodb://localhost", dbName: "test" },
+    redis: {},
+  },
+}))
+
+import schema from "../schema"
+
+it("builds the schema without error", () => {
+  expect(schema).toBeDefined()
+  expect(schema.getQueryType()).toBeDefined()
+  expect(schema.getMutationType()).toBeDefined()
+})

packages/openneuro-server/src/graphql/__tests__/schema.spec.ts

@@ -0,0 +1,42 @@
+import SchemaBuilder from "@pothos/core"
+import SimpleObjectsPlugin from "@pothos/plugin-simple-objects"
+import DirectivesPlugin from "@pothos/plugin-directives"
+
+export interface UserInfo {
+  id: string
+  userId: string
+  admin: boolean
+  username?: string
+  provider?: string
+  providerId?: string
+  blocked?: boolean
+  orcidConsent?: boolean | null
+  reviewer?: boolean
+  exp?: string
+  scopes?: string[]
+  indexer?: boolean
+}
+
+export interface GraphQLContext {
+  user: string
+  userInfo: UserInfo
+}
+
+export const builder = new SchemaBuilder<{
+  Context: GraphQLContext
+  Scalars: {
+    ID: { Input: string; Output: string }
+    Date: { Input: string; Output: Date }
+    DateTime: { Input: string; Output: Date }
+    BigInt: { Input: number; Output: number }
+    JSON: { Input: unknown; Output: unknown }
+  }
+  DefaultFieldNullability: true
+}>({
+  plugins: [SimpleObjectsPlugin, DirectivesPlugin],
+  notStrict:
+    "Pothos may not work correctly when strict mode is not enabled in tsconfig.json",
+  directives: {
+    useGraphQLToolsUnorderedDirectives: true,
+  },
+})

packages/openneuro-server/src/graphql/builder.ts

@@ -21,7 +21,10 @@ describe("dataset resolvers", () => {
       const { id: dsId } = await ds.createDataset(
         null,
         { affirmedDefaced: true, affirmedConsent: false },
-        { user: "123456", userInfo: {} },
+        {
+          user: "123456",
+          userInfo: { id: "123456", userId: "123456", admin: false },
+        },
       )
       expect(dsId).toEqual(expect.stringMatching(/^ds[0-9]{6}$/))
     })
@@ -170,6 +173,8 @@ describe("dataset resolvers", () => {
           user: "a_user_id",
           userInfo: {
             // bypass permission checks
+            id: "a_user_id",
+            userId: "a_user_id",
             admin: true,
           },
         },

packages/openneuro-server/src/graphql/resolvers/__tests__/dataset.spec.ts

@@ -1,5 +1,6 @@
 import { vi } from "vitest"
 import { allowedImportUrl, importRemoteDataset } from "../importRemoteDataset"
+import type { GraphQLContext } from "../../builder"
 
 vi.mock("ioredis")
 vi.mock("../../../config")
@@ -10,7 +11,7 @@ describe("importRemoteDataset mutation", () => {
     await importRemoteDataset(
       {},
       { datasetId: "ds000000", url: "" },
-      { user: "1234", userInfo: { admin: true } },
+      { user: "1234", userInfo: { admin: true } } as GraphQLContext,
     )
   })
   describe("allowedImportUrl()", () => {