@openneuro/server 5.1.1 → 5.1.3

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openneuro/server",
-  "version": "5.1.1",
+  "version": "5.1.3",
   "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": "^5.1.1",
+    "@openneuro/search": "^5.1.3",
     "@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": "035b0b4544d4b287506ea00aff3b424ed816611a"
+  "gitHead": "b1059b286940adb3b60150217e691fe75a895d94"
 }

package/src/graphql/resolvers/snapshots.ts

@@ -54,7 +54,6 @@ export const snapshot = (obj, { datasetId, tag }, context: GraphQLContext) => {
     () => {
       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),

package/src/libs/doi/__tests__/metadata.spec.ts

@@ -0,0 +1,149 @@
+import { beforeEach, describe, expect, it, vi } from "vitest"
+import { assembleMetadata } from "../metadata.js"
+
+vi.mock("ioredis")
+vi.mock("../../../config", () => ({
+  default: { url: "https://openneuro.org" },
+}))
+vi.mock("../index", () => ({
+  createDOI: (datasetId: string, snapshotId: string) =>
+    `10.18112/openneuro.${datasetId}.v${snapshotId}`,
+}))
+vi.mock("../../../utils/datacite-utils")
+vi.mock("../../../datalad/description")
+vi.mock("../../../graphql/resolvers/summary")
+
+import { getDataciteYml } from "../../../utils/datacite-utils.js"
+import { description } from "../../../datalad/description.js"
+
+const mockGetDataciteYml = vi.mocked(getDataciteYml)
+const mockDescription = vi.mocked(description)
+
+const baseYml = {
+  data: {
+    attributes: {
+      creators: [{ name: "Doe, Jane", nameType: "Personal" }],
+      titles: [{ title: "Test Dataset" }],
+    },
+  },
+}
+
+const baseDesc = {
+  Name: "Test Dataset",
+  Authors: [],
+}
+
+beforeEach(() => {
+  vi.resetAllMocks()
+  mockDescription.mockResolvedValue(baseDesc as never)
+})
+
+describe("assembleMetadata", () => {
+  describe("contributor name validation", () => {
+    it("keeps a contributor whose name has one comma (surname, given)", async () => {
+      mockGetDataciteYml.mockResolvedValue({
+        ...baseYml,
+        data: {
+          attributes: {
+            ...baseYml.data.attributes,
+            contributors: [
+              { name: "Doe, Jane", contributorType: "DataCollector" },
+            ],
+          },
+        },
+      } as never)
+
+      const result = await assembleMetadata("ds000001", "1.0.0")
+      expect(result.contributors).toHaveLength(1)
+      expect(result.contributors![0].name).toBe("Doe, Jane")
+    })
+
+    it("keeps a contributor whose name has no comma", async () => {
+      mockGetDataciteYml.mockResolvedValue({
+        ...baseYml,
+        data: {
+          attributes: {
+            ...baseYml.data.attributes,
+            contributors: [
+              { name: "OpenNeuro Team", contributorType: "HostingInstitution" },
+            ],
+          },
+        },
+      } as never)
+
+      const result = await assembleMetadata("ds000001", "1.0.0")
+      expect(result.contributors).toHaveLength(1)
+      expect(result.contributors![0].name).toBe("OpenNeuro Team")
+    })
+
+    it("strips a contributor whose name contains more than one comma", async () => {
+      mockGetDataciteYml.mockResolvedValue({
+        ...baseYml,
+        data: {
+          attributes: {
+            ...baseYml.data.attributes,
+            contributors: [
+              {
+                name: "Doe, Jane, Smith, John",
+                contributorType: "DataCollector",
+              },
+            ],
+          },
+        },
+      } as never)
+
+      const result = await assembleMetadata("ds000001", "1.0.0")
+      expect(result.contributors).toBeUndefined()
+    })
+
+    it("strips only the invalid contributor and keeps the valid ones", async () => {
+      mockGetDataciteYml.mockResolvedValue({
+        ...baseYml,
+        data: {
+          attributes: {
+            ...baseYml.data.attributes,
+            contributors: [
+              { name: "Doe, Jane", contributorType: "DataCollector" },
+              {
+                name: "Smith, John, Doe, Jane",
+                contributorType: "DataCollector",
+              },
+              { name: "Williams, Bob", contributorType: "DataManager" },
+            ],
+          },
+        },
+      } as never)
+
+      const result = await assembleMetadata("ds000001", "1.0.0")
+      expect(result.contributors).toHaveLength(2)
+      expect(result.contributors!.map((c) => c.name)).toEqual([
+        "Doe, Jane",
+        "Williams, Bob",
+      ])
+    })
+  })
+
+  describe("contributor field stripping", () => {
+    it("removes the order field from contributors", async () => {
+      mockGetDataciteYml.mockResolvedValue({
+        ...baseYml,
+        data: {
+          attributes: {
+            ...baseYml.data.attributes,
+            contributors: [
+              {
+                name: "Doe, Jane",
+                contributorType: "DataCollector",
+                order: 1,
+              },
+            ],
+          },
+        },
+      } as never)
+
+      const result = await assembleMetadata("ds000001", "1.0.0")
+      expect(result.contributors).toHaveLength(1)
+      expect(result.contributors![0]).not.toHaveProperty("order")
+    })
+  })
+})

package/src/libs/doi/metadata.ts

@@ -37,21 +37,33 @@ export async function assembleMetadata(
   let contributors: DataCite["contributors"]
   let resourceType: string | undefined
 
+  const desc = await description({
+    id: datasetId,
+    revision: revision || "HEAD",
+  })
+
   if (hasDataciteCreators) {
-    // Use datacite.yml metadata
     creators = ymlAttrs.creators
-    titles = ymlAttrs.descriptions?.length
-      ? [{ title: ymlAttrs.descriptions[0].description }]
-      : []
+    titles = ymlAttrs.titles?.length
+      ? ymlAttrs.titles
+      : [{ title: desc.Name || datasetId }]
     descriptions = ymlAttrs.descriptions
+    // Strip empty givenName/familyName and the internal `order` field.
+    // Also filter out contributors whose name contains more than one comma,
+    // which indicates multiple names were concatenated into a single string.
     contributors = ymlAttrs.contributors
+      ?.filter((c) => (c.name?.split(",").length ?? 1) <= 2)
+      .map((c) => {
+        const { givenName, familyName, order: _order, ...rest } = c
+        return {
+          ...rest,
+          ...(givenName?.trim() ? { givenName } : {}),
+          ...(familyName?.trim() ? { familyName } : {}),
+        }
+      })
     resourceType = ymlAttrs.types?.resourceType
   } else {
     // Fall back to BIDS dataset_description.json
-    const desc = await description({
-      id: datasetId,
-      revision: revision || "HEAD",
-    })
     creators = (desc.Authors || [])
       .filter((author: string) => author)
       .map((author: string) => ({
@@ -66,15 +78,6 @@ export async function assembleMetadata(
     resourceType = await getPrimaryModality(datasetId)
   }
 
-  // If datacite.yml had titles via a different path, use them
-  if (hasDataciteCreators && titles.length === 0) {
-    const desc = await description({
-      id: datasetId,
-      revision: revision || "HEAD",
-    })
-    titles = [{ title: desc.Name || datasetId }]
-  }
-
   const attributes: DataCite = {
     doi,
     url,

package/src/types/datacite.ts

@@ -70,7 +70,7 @@ export interface RawDataciteYml {
     attributes: Partial<
       Pick<
         DataCite,
-        "contributors" | "creators" | "types" | "descriptions"
+        "contributors" | "creators" | "types" | "descriptions" | "titles"
       >
     >
   }