@openneuro/server 4.28.3 → 4.29.0-alpha.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openneuro/server",
-  "version": "4.28.3",
+  "version": "4.29.0-alpha.1",
   "description": "Core service for the OpenNeuro platform.",
   "license": "MIT",
   "main": "src/server.js",
@@ -15,13 +15,13 @@
   },
   "author": "Squishymedia",
   "dependencies": {
-    "@apollo/client": "3.7.2",
+    "@apollo/client": "3.11.8",
     "@apollo/server": "4.9.3",
     "@apollo/utils.keyvadapter": "3.0.0",
     "@elastic/elasticsearch": "8.13.1",
     "@graphql-tools/schema": "^10.0.0",
     "@keyv/redis": "^2.7.0",
-    "@openneuro/search": "^4.28.3",
+    "@openneuro/search": "^4.29.0-alpha.1",
     "@sentry/node": "^8.25.0",
     "@sentry/profiling-node": "^8.25.0",
     "base64url": "^3.0.0",
@@ -30,7 +30,7 @@
     "date-fns": "^2.16.1",
     "draft-js": "^0.11.7",
     "draft-js-export-html": "^1.4.1",
-    "express": "4.19.2",
+    "express": "4.20.0",
     "graphql": "16.8.1",
     "graphql-bigint": "^1.0.0",
     "graphql-compose": "9.0.10",
@@ -59,8 +59,8 @@
     "semver": "^5.5.0",
     "sitemap": "^2.1.0",
     "superagent": "^3.8.2",
-    "ts-node": "9.1.1",
-    "typescript": "5.1.6",
+    "ts-node": "10.9.2",
+    "typescript": "5.6.3",
     "underscore": "^1.8.3",
     "uuid": "10.0.0",
     "xmldoc": "^1.1.0"
@@ -79,11 +79,11 @@
     "nodemon": "3.1.0",
     "ts-node-dev": "1.1.6",
     "tsc-watch": "^4.2.9",
-    "vitest": "1.5.0",
-    "vitest-fetch-mock": "0.2.2"
+    "vitest": "2.1.2",
+    "vitest-fetch-mock": "0.3.0"
   },
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "54302c961cba3420d7bac9dcf67010b78d430651"
+  "gitHead": "6c4cb2bde08a8a0cbead95d505a7d002290fdb5b"
 }

package/src/app.ts

@@ -1,6 +1,4 @@
 /*eslint no-console: ["error", { allow: ["log"] }] */
-/* eslint-disable no-unused-vars*/
-
 /**
  * Express app setup
  */

package/src/cache/item.ts

@@ -1,7 +1,7 @@
-import { Redis } from "ioredis"
+import type { Redis } from "ioredis"
 import * as zlib from "zlib"
 import { promisify } from "util"
-import { CacheType } from "./types"
+import type { CacheType } from "./types"
 export { CacheType } from "./types"
 
 const compress = promisify(zlib.gzip)
@@ -13,7 +13,7 @@ const decompress = promisify(zlib.gunzip)
  */
 export function cacheKey(
   type: CacheType,
-  compositeKeys: Array<string>,
+  compositeKeys: string[],
 ): string {
   return `${type.toString()}:${compositeKeys.join(":")}`
 }
@@ -35,7 +35,7 @@ class CacheItem {
   constructor(
     redis: Redis,
     type: CacheType,
-    compositeKeys?: Array<string>,
+    compositeKeys?: string[],
     expiration?: number,
   ) {
     this.redis = redis

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

@@ -11,31 +11,6 @@ vi.mock("../../config.ts")
 
 const filename = "sub-01/anat/sub-01_T1w.nii.gz"
 
-const mockRootFiles = [
-  { filename: "README" },
-  { filename: "dataset_description.json" },
-]
-const mockSub01 = [
-  { filename: "sub-01/anat/sub-01_T1w.nii.gz" },
-  { filename: "sub-01/func/sub-01_task-onebacktask_run-01_bold.nii.gz" },
-]
-const mockSub02 = [
-  { filename: "sub-02/anat/sub-02_T1w.nii.gz" },
-  { filename: "sub-02/func/sub-02_task-onebacktask_run-01_bold.nii.gz" },
-]
-const mockSub03 = [
-  { filename: "sub-03/anat/sub-03_T1w.nii.gz" },
-  { filename: "sub-03/func/sub-03_task-onebacktask_run-01_bold.nii.gz" },
-]
-const mockDerivatives = [{ filename: "derivatives/groundbreaking_output.html" }]
-const mockFiles = [
-  ...mockRootFiles,
-  ...mockSub01,
-  ...mockSub02,
-  ...mockSub03,
-  ...mockDerivatives,
-]
-
 describe("datalad files", () => {
   describe("encodeFilePath()", () => {
     it("should encode a nested path", () => {

package/src/datalad/analytics.ts

@@ -1,4 +1,3 @@
-import Analytics from "../models/analytics"
 import Dataset from "../models/dataset"
 
 /**

package/src/datalad/dataset.ts

@@ -7,7 +7,7 @@ import request from "superagent"
 import requestNode from "request"
 import objectHash from "object-hash"
 import { Readable } from "stream"
-import * as Mongoose from "mongoose"
+import type * as Mongoose from "mongoose"
 import config from "../config"
 import * as subscriptions from "../handlers/subscriptions"
 import { generateDataladCookie } from "../libs/authentication/jwt"
@@ -69,15 +69,26 @@ export const createDataset = async (
   }
 }
 
+interface WorkerDraftFields {
+  // Commit id hash
+  ref: string
+  // Commit tree ref
+  tree: string
+  // Commit message
+  message: string
+  // Commit author time
+  modified: string
+}
+
 /**
  * Return the latest commit
  * @param {string} id Dataset accession number
  */
-export const getDraftHead = async (id) => {
+export const getDraftHead = async (id): Promise<WorkerDraftFields> => {
   const draftRes = await request
     .get(`${getDatasetWorker(id)}/datasets/${id}/draft`)
     .set("Accept", "application/json")
-  return draftRes.body.hexsha
+  return draftRes.body
 }
 
 /**
@@ -87,7 +98,7 @@ export const getDataset = async (id) => {
   const dataset = await Dataset.findOne({ id }).lean()
   return {
     ...dataset,
-    revision: await getDraftHead(id),
+    revision: (await getDraftHead(id)).ref,
   }
 }
 
@@ -378,7 +389,6 @@ export const addFileString = (datasetId, filename, mimetype, content) =>
     // Mock a stream so we can reuse addFile
     createReadStream: () => {
       const stream = new Readable()
-      // eslint-disable-next-line @typescript-eslint/unbound-method
       stream._read = () => {
         // Content is available already, _read does nothing
       }
@@ -406,7 +416,7 @@ export const commitFiles = (datasetId, user) => {
     .set("Accept", "application/json")
     .then((res) => {
       gitRef = res.body.ref
-      return updateDatasetRevision(datasetId, gitRef).then(() => gitRef)
+      return updateDatasetRevision(datasetId).then(() => gitRef)
     })
 }
 
@@ -495,7 +505,7 @@ export const updatePublic = (datasetId, publicFlag) =>
     { upsert: true },
   ).exec()
 
-export const getDatasetAnalytics = (datasetId, tag) => {
+export const getDatasetAnalytics = (datasetId, _tag) => {
   return Dataset.findOne({ id: datasetId }).then((ds) => ({
     datasetId,
     views: ds.views || 0,

package/src/datalad/description.ts

@@ -38,58 +38,58 @@ export const repairDescriptionTypes = (description) => {
   const newDescription = { ...description }
   // Array types
   if (
-    description.hasOwnProperty("Authors") &&
+    Object.hasOwn(description, "Authors") &&
     !Array.isArray(description.Authors)
   ) {
     newDescription.Authors = [description.Authors]
   }
   if (
-    description.hasOwnProperty("ReferencesAndLinks") &&
+    Object.hasOwn(description, "ReferencesAndLinks") &&
     !Array.isArray(description.ReferencesAndLinks)
   ) {
     newDescription.ReferencesAndLinks = [description.ReferencesAndLinks]
   }
   if (
-    description.hasOwnProperty("Funding") &&
+    Object.hasOwn(description, "Funding") &&
     !Array.isArray(description.Funding)
   ) {
     newDescription.Funding = [description.Funding]
   }
   if (
-    description.hasOwnProperty("EthicsApprovals") &&
+    Object.hasOwn(description, "EthicsApprovals") &&
     !Array.isArray(description.EthicsApprovals)
   ) {
     newDescription.EthicsApprovals = [description.EthicsApprovals]
   }
   // String types
   if (
-    description.hasOwnProperty("Name") &&
+    Object.hasOwn(description, "Name") &&
     typeof description.Name !== "string"
   ) {
     newDescription.Name = JSON.stringify(description.Name) || ""
   }
   if (
-    description.hasOwnProperty("DatasetDOI") &&
+    Object.hasOwn(description, "DatasetDOI") &&
     typeof description.DatasetDOI !== "string"
   ) {
     newDescription.DatasetDOI = JSON.stringify(description.DatasetDOI) || ""
   }
   if (
-    description.hasOwnProperty("Acknowledgements") &&
+    Object.hasOwn(description, "Acknowledgements") &&
     typeof description.Acknowledgements !== "string"
   ) {
     newDescription.Acknowledgements =
       JSON.stringify(description.Acknowledgements) || ""
   }
   if (
-    description.hasOwnProperty("HowToAcknowledge") &&
+    Object.hasOwn(description, "HowToAcknowledge") &&
     typeof description.HowToAcknowledge !== "string"
   ) {
     newDescription.HowToAcknowledge =
       JSON.stringify(description.HowToAcknowledge) || ""
   }
   if (
-    description.hasOwnProperty("DatasetType") &&
+    Object.hasOwn(description, "DatasetType") &&
     typeof description.DatasetType !== "string"
   ) {
     newDescription.DatasetType = "raw"
@@ -104,7 +104,7 @@ export const appendSeniorAuthor = (description) => {
   try {
     const SeniorAuthor = description?.Authors[description.Authors.length - 1]
     return { ...description, SeniorAuthor }
-  } catch (err) {
+  } catch (_err) {
     return description
   }
 }
@@ -132,7 +132,7 @@ export const description = async (obj) => {
       )
     })
     return appendSeniorAuthor(repairDescriptionTypes(datasetDescription))
-  } catch (err) {
+  } catch (_err) {
     return defaultDescription
   }
 }

package/src/datalad/draft.ts

@@ -21,7 +21,7 @@ export const getDraftRevision = async (datasetId) => {
   })
 }
 
-export const updateDatasetRevision = (datasetId, gitRef) => {
+export const updateDatasetRevision = (datasetId) => {
   /**
    * Update the revision modified time in a draft on changes
    */

package/src/datalad/pagination.ts

@@ -43,10 +43,10 @@ export const maxLimit = (limit) => Math.max(Math.min(limit, 100), 1)
 
 // Decode cursor from options object
 export const getOffsetFromCursor = (options) => {
-  if (options.hasOwnProperty("after") && options.after) {
+  if (Object.hasOwn(options, "after") && options.after) {
     return decodeCursor(options.after).offset
   }
-  if (options.hasOwnProperty("before") && options.before) {
+  if (Object.hasOwn(options, "before") && options.before) {
     return (
       decodeCursor(options.before).offset - Math.max(maxLimit(options.first), 0)
     )
@@ -63,7 +63,7 @@ export const getOffsetFromCursor = (options) => {
 export const sortAggregate = (options) => {
   const sortingStages = []
   const finalSort = {}
-  if (options.hasOwnProperty("orderBy")) {
+  if (Object.hasOwn(options, "orderBy")) {
     if ("created" in options.orderBy && options.orderBy.created) {
       finalSort["_id"] = sortEnumToInt(options.orderBy.created)
     }

package/src/datalad/snapshots.ts

@@ -1,6 +1,7 @@
 /**
  * Get snapshots from datalad-service tags
  */
+import * as Sentry from "@sentry/node"
 import request from "superagent"
 import { reindexDataset } from "../elasticsearch/reindex-dataset"
 import { redis, redlock } from "../libs/redis"
@@ -16,7 +17,8 @@ import { getFiles } from "./files"
 import { generateDataladCookie } from "../libs/authentication/jwt"
 import notifications from "../libs/notifications"
 import Dataset from "../models/dataset"
-import Snapshot, { SnapshotDocument } from "../models/snapshot"
+import Snapshot from "../models/snapshot"
+import type { SnapshotDocument } from "../models/snapshot"
 import { updateDatasetRevision } from "./draft"
 import { getDatasetWorker } from "../libs/datalad-service"
 import { join } from "path"
@@ -62,6 +64,8 @@ const createIfNotExistsDoi = async (
         descriptionFieldUpdates["DatasetDOI"] = `doi:${snapshotDoi}`
       }
     } catch (err) {
+      Sentry.captureException(err)
+      // eslint-disable-next-line no-console
       console.error(err)
       throw new Error("DOI minting failed.")
     }
@@ -154,7 +158,7 @@ export const createSnapshot = async (
 
     await Promise.all([
       // Update the draft status in datasets collection in case any changes were made (DOI, License)
-      updateDatasetRevision(datasetId, snapshot.hexsha),
+      updateDatasetRevision(datasetId),
 
       // Update metadata in snapshots collection
       createSnapshotMetadata(datasetId, tag, snapshot.hexsha, snapshot.created),

package/src/elasticsearch/reindex-dataset.ts

@@ -1,12 +1,8 @@
 import config from "../config"
 import { indexDataset, indexingToken, queryForIndex } from "@openneuro/search"
 import { elasticClient } from "./elastic-client"
-import {
-  ApolloClient,
-  from,
-  InMemoryCache,
-  NormalizedCacheObject,
-} from "@apollo/client"
+import { ApolloClient, from, InMemoryCache } from "@apollo/client"
+import type { NormalizedCacheObject } from "@apollo/client"
 import { setContext } from "@apollo/client/link/context"
 import { HttpLink } from "@apollo/client/link/http"
 

package/src/graphql/permissions.ts

@@ -67,7 +67,7 @@ export class DeletedDatasetError extends GraphQLError {
           // Only return a relative path to avoid cross site risks
           extensions = { code: "DELETED_DATASET", redirect: url.pathname }
         }
-      } catch (err) {
+      } catch (_err) {
         // Do nothing
       }
     }

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

@@ -1,5 +1,5 @@
 import { vi } from "vitest"
-import { HasId } from "../../../utils/datasetOrSnapshot"
+import type { HasId } from "../../../utils/datasetOrSnapshot"
 import { brainlifeQuery } from "../brainlife"
 
 vi.mock("ioredis")

package/src/graphql/resolvers/brainlife.ts

@@ -1,7 +1,5 @@
-import {
-  DatasetOrSnapshot,
-  getDatasetFromSnapshotId,
-} from "../../utils/datasetOrSnapshot"
+import { getDatasetFromSnapshotId } from "../../utils/datasetOrSnapshot"
+import type { DatasetOrSnapshot } from "../../utils/datasetOrSnapshot"
 
 interface BrainlifeFindQuery {
   removed: boolean
@@ -52,7 +50,7 @@ export const onBrainlife = async (
     } else {
       return false
     }
-  } catch (err) {
+  } catch (_err) {
     return false
   }
 }

package/src/graphql/resolvers/cache.ts

@@ -19,7 +19,7 @@ export async function cacheClear(
     try {
       await downloadCache.drop()
       return true
-    } catch (err) {
+    } catch (_err) {
       return false
     }
   } else {

package/src/graphql/resolvers/dataset-search.ts

@@ -1,10 +1,10 @@
+import * as Sentry from "@sentry/node"
 import { elasticClient } from "../../elasticsearch/elastic-client"
 import { dataset } from "./dataset"
 import Star from "../../models/stars"
 import Subscription from "../../models/subscription"
 import Permission from "../../models/permission"
 import { hashObject } from "../../libs/authentication/crypto"
-import util from "util"
 
 const elasticIndex = "datasets"
 
@@ -70,7 +70,7 @@ export const elasticRelayConnection = (
       },
     }
   } catch (err) {
-    console.error(err)
+    Sentry.captureException(err)
   }
 }
 
@@ -95,11 +95,11 @@ export const datasetSearchConnection = async (
   if (after) {
     try {
       requestBody.search_after = decodeCursor(after)
-    } catch (err) {
+    } catch (_err) {
       // Don't include search_after if parsing fails
     }
   }
-  const result = await elasticClient.search({
+  await elasticClient.search({
     index: elasticIndex,
     size: first,
     q: `${q} AND public:true`,

package/src/graphql/resolvers/dataset.ts

@@ -125,6 +125,7 @@ export const deleteDataset = async (
     await removeDatasetSearchDocument(id)
   } catch (err) {
     // This likely means this dataset had not yet been indexed
+    /* eslint-disable-next-line no-console */
     console.error(err)
   }
   await new Deletion({
@@ -146,9 +147,9 @@ export const deleteFiles = async (
 ) => {
   try {
     await checkDatasetWrite(datasetId, user, userInfo)
-    const deletedFiles = await datalad.deleteFiles(datasetId, files, userInfo)
+    await datalad.deleteFiles(datasetId, files, userInfo)
     return true
-  } catch (err) {
+  } catch (_err) {
     return false
   }
 }
@@ -169,7 +170,7 @@ export const removeAnnexObject = async (
       userInfo,
     )
     return true
-  } catch (err) {
+  } catch (_err) {
     return false
   }
 }
@@ -189,7 +190,7 @@ export const flagAnnexObject = async (
       userInfo,
     )
     return true
-  } catch (err) {
+  } catch (_err) {
     return false
   }
 }
@@ -228,7 +229,7 @@ export const trackAnalytics = (obj, { datasetId, tag, type }) => {
   try {
     dataladAnalytics.trackAnalytics(datasetId, tag, type)
     return true
-  } catch (err) {
+  } catch (_err) {
     return false
   }
 }
@@ -276,11 +277,14 @@ const worker = (obj) => getDatasetWorker(obj.id)
  */
 const Dataset = {
   uploader: (ds) => user(ds, { id: ds.uploader }),
-  draft: async (obj) => ({
-    id: obj.id,
-    revision: await datalad.getDraftHead(obj.id),
-    modified: obj.modified,
-  }),
+  draft: async (obj) => {
+    const draftHead = await datalad.getDraftHead(obj.id)
+    return {
+      id: obj.id,
+      revision: draftHead.ref,
+      modified: draftHead.modified,
+    }
+  },
   snapshots,
   latestSnapshot,
   analytics,

package/src/graphql/resolvers/derivatives.ts

@@ -1,8 +1,6 @@
-import {
-  DatasetOrSnapshot,
-  getDatasetFromSnapshotId,
-} from "../../utils/datasetOrSnapshot"
+import { getDatasetFromSnapshotId } from "../../utils/datasetOrSnapshot"
 import config from "../../config"
+import type { DatasetOrSnapshot } from "../../utils/datasetOrSnapshot"
 
 const S3_BUCKET = "openneuro-derivatives"
 const GITHUB_ORGANIZATION = "OpenNeuroDerivatives"
@@ -44,7 +42,7 @@ export const githubDerivative = async (
       }
     }
     return false
-  } catch (err) {
+  } catch (_err) {
     return false
   }
 }
@@ -78,14 +76,14 @@ export const derivativeObject = (
  */
 export const derivatives = async (
   dataset: DatasetOrSnapshot,
-): Promise<Array<DatasetDerivatives>> => {
+): Promise<DatasetDerivatives[]> => {
   let datasetId
   if ("tag" in dataset) {
     datasetId = getDatasetFromSnapshotId(dataset.id)
   } else {
     datasetId = dataset.id
   }
-  const available: Array<DatasetDerivatives> = []
+  const available: DatasetDerivatives[] = []
   if (await githubDerivative(datasetId, "mriqc")) {
     available.push(derivativeObject(datasetId, "mriqc"))
   }

package/src/graphql/resolvers/draft.ts

@@ -3,10 +3,11 @@ import { summary } from "./summary"
 import { issues } from "./issues.js"
 import { description } from "./description.js"
 import { readme } from "./readme.js"
-import { getDraftRevision, updateDatasetRevision } from "../../datalad/draft.js"
+import { getDraftRevision } from "../../datalad/draft.js"
 import { checkDatasetWrite } from "../permissions.js"
 import { getFiles } from "../../datalad/files"
 import { filterRemovedAnnexObjects } from "../utils/file.js"
+import { validation } from "./validation"
 
 // A draft must have a dataset parent
 const draftFiles = async (dataset, args, { userInfo }) => {
@@ -15,6 +16,7 @@ const draftFiles = async (dataset, args, { userInfo }) => {
   return filterRemovedAnnexObjects(dataset.id, userInfo)(files)
 }
 
+/* eslint-disable-next-line @typescript-eslint/no-unused-vars */
 const draftSize = async (dataset, args, { userInfo }) => {
   const hexsha = await getDraftRevision(dataset.id)
   return Summary.findOne({ datasetId: dataset.id, id: hexsha })
@@ -22,20 +24,6 @@ const draftSize = async (dataset, args, { userInfo }) => {
     .then((res) => res?.toObject()?.size)
 }
 
-/**
- * Deprecated mutation to move the draft HEAD reference forward or backward
- *
- * Exists to support existing usage where this would result in the initial snapshot
- */
-export const updateRef = async (
-  obj,
-  { datasetId, ref },
-  { user, userInfo },
-) => {
-  await checkDatasetWrite(datasetId, user, userInfo)
-  await updateDatasetRevision(datasetId, ref)
-}
-
 /**
  * Mutation to move the draft HEAD reference forward or backward
  */
@@ -49,6 +37,7 @@ const draft = {
   size: draftSize,
   summary,
   issues,
+  validation,
   modified: (obj) => obj.modified,
   description,
   readme,

package/src/graphql/resolvers/importRemoteDataset.ts

@@ -65,6 +65,7 @@ export async function importRemoteDataset(
 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> },
 ): Promise<boolean> {
   const ingest = await IngestDataset.findById(id)

package/src/graphql/resolvers/metadata.ts

@@ -1,7 +1,8 @@
 import Snapshot from "../../models/snapshot"
-import { LeanDocument } from "mongoose"
+import type { LeanDocument } from "mongoose"
 import DatasetModel from "../../models/dataset"
-import MetadataModel, { MetadataDocument } from "../../models/metadata"
+import MetadataModel from "../../models/metadata"
+import type { MetadataDocument } from "../../models/metadata"
 import { latestSnapshot } from "./snapshots"
 import { permissions } from "./permissions"
 
@@ -71,8 +72,8 @@ export const addMetadata = async (obj, { datasetId, metadata }) => {
  * Resolve all public datasets and return metadata
  */
 export async function publicMetadata(
-  obj,
-): Promise<Array<LeanDocument<MetadataDocument>>> {
+  _obj,
+): Promise<LeanDocument<MetadataDocument>[]> {
   const datasets = await DatasetModel.find({
     public: true,
   }).lean()