@openneuro/server 4.47.7 → 5.0.0-alpha.0

package/src/graphql/resolvers/datasetEvents.ts

@@ -1,12 +1,10 @@
 import DatasetEvent from "../../models/datasetEvents"
+import { toDbStatus, toGraphqlStatus } from "./response-status"
+import type { DbStatus, GraphqlStatus } from "./response-status"
 import User from "../../models/user"
-import type { UserDocument } from "../../models/user"
 import { checkDatasetAdmin } from "../permissions"
 import type {
-  DatasetEventContributorCitation,
-  DatasetEventContributorCitationResponse,
   DatasetEventContributorRequest,
-  DatasetEventContributorRequestResponse,
   DatasetEventDocument,
 } from "../../models/datasetEvents"
 import { UserNotificationStatus } from "../../models/userNotificationStatus"
@@ -24,34 +22,12 @@ function isContributorRequest(
   return event.event.type === "contributorRequest"
 }
 
-function isContributorCitation(
-  event: DatasetEventDocument,
-): event is DatasetEventDocument & { event: DatasetEventContributorCitation } {
-  return event.event.type === "contributorCitation"
-}
-
-function isContributorRequestResponse(
-  event: DatasetEventDocument,
-): event is DatasetEventDocument & {
-  event: DatasetEventContributorRequestResponse
-} {
-  return event.event.type === "contributorRequestResponse"
-}
-
-function isContributorCitationResponse(
-  event: DatasetEventDocument,
-): event is DatasetEventDocument & {
-  event: DatasetEventContributorCitationResponse
-} {
-  return event.event.type === "contributorCitationResponse"
-}
-
 /** Enriched type for GraphQL */
 export type EnrichedDatasetEvent =
   & Omit<DatasetEventDocument, "notificationStatus">
   & {
     hasBeenRespondedTo?: boolean
-    responseStatus?: "pending" | "accepted" | "denied" | null
+    responseStatus?: DbStatus | null
     notificationStatus?: UserNotificationStatusDocument
   }
 
@@ -81,11 +57,11 @@ export async function datasetEvents(
       }) as UserNotificationStatusDocument
     }
 
+    // Internal representation stays lowercase (DbStatus) here; the
+    // GraphQL resolver edge (DatasetEventTypeResolvers in ./index.ts)
+    // converts to the uppercase ResponseStatusType enum at query time.
     if ("resolutionStatus" in e.event) {
-      ev.responseStatus = e.event.resolutionStatus as
-        | "pending"
-        | "accepted"
-        | "denied"
+      ev.responseStatus = e.event.resolutionStatus as DbStatus
       ev.hasBeenRespondedTo = ev.responseStatus !== null &&
         ev.responseStatus !== "pending"
     } else {
@@ -103,51 +79,29 @@ export async function datasetEvents(
   )
 }
 
-// --- Field-level resolvers ---
-export const DatasetEventResolvers = {
-  hasBeenRespondedTo: (ev: EnrichedDatasetEvent) =>
-    ev.hasBeenRespondedTo ?? false,
-  responseStatus: (ev: EnrichedDatasetEvent) => ev.responseStatus ?? null,
-  notificationStatus: (ev: EnrichedDatasetEvent) =>
-    ev.notificationStatus?.status ?? "UNREAD",
-  requestId: (ev: EnrichedDatasetEvent) =>
-    isContributorRequest(ev) || isContributorRequestResponse(ev)
-      ? ev.event.requestId
-      : null,
-  target: async (ev: EnrichedDatasetEvent): Promise<UserDocument | null> => {
-    const targetUserId = isContributorRequestResponse(ev) ||
-        isContributorCitation(ev) ||
-        isContributorCitationResponse(ev)
-      ? ev.event.targetUserId
-      : undefined
-
-    if (!targetUserId) return null
-    // Use findOne({ id }) for UUID strings
-    return User.findOne({ id: targetUserId })
-  },
-  user: async (ev: EnrichedDatasetEvent): Promise<UserDocument | null> =>
-    ev.userId ? User.findOne({ id: ev.userId }) : null,
-  contributorData: (ev: EnrichedDatasetEvent) => {
-    let data: DatasetEventContributorCitation["contributorData"] | undefined
-
-    if (
-      (isContributorCitation(ev) || isContributorCitationResponse(ev)) &&
-      ev.event.contributorData
-    ) {
-      data = ev.event.contributorData
-    } else if (
-      (isContributorRequest(ev) || isContributorRequestResponse(ev)) &&
-      ev.event.contributorData
-    ) {
-      data = ev.event.contributorData
-    }
+/**
+ * Minimal type-level resolvers wired via ./index.ts. These exist so the
+ * case conversion for resolutionStatus / responseStatus runs at the
+ * GraphQL edge, regardless of which query/mutation produced the event
+ * object. Only the status-related fields are declared here; every other
+ * field of DatasetEvent and DatasetEventDescription continues to resolve
+ * via default property access.
+ */
+export const DatasetEventTypeResolvers = {
+  responseStatus: (
+    ev: { responseStatus?: DbStatus | null },
+  ): GraphqlStatus | null => toGraphqlStatus(ev.responseStatus),
+  hasBeenRespondedTo: (
+    ev: { hasBeenRespondedTo?: boolean },
+  ): boolean => ev.hasBeenRespondedTo ?? false,
+}
 
-    return {
-      ...data,
-      contributorType: data?.contributorType || "Researcher",
-    }
-  },
+export const DatasetEventDescriptionTypeResolvers = {
+  resolutionStatus: (
+    evDesc: { resolutionStatus?: DbStatus | null },
+  ): GraphqlStatus | null => toGraphqlStatus(evDesc.resolutionStatus),
 }
+
 /**
  * Create a 'contributor request' event
  */
@@ -235,13 +189,13 @@ export async function processContributorRequest(
     datasetId,
     requestId,
     targetUserId,
-    resolutionStatus,
+    resolutionStatus: graphqlResolutionStatus,
     reason,
   }: {
     datasetId: string
     requestId: string
     targetUserId: string
-    resolutionStatus: "accepted" | "denied"
+    resolutionStatus: "ACCEPTED" | "DENIED"
     reason?: string
   },
   { user: currentUserId, userInfo }: {
@@ -253,6 +207,14 @@ export async function processContributorRequest(
     throw new Error("Authentication required to process contributor requests.")
   }
 
+  const resolutionStatus = toDbStatus(graphqlResolutionStatus)
+
+  // Note that this is technically possible with hand-crafted GraphQL
+  // Separating types in the schema will enforce this at the endpoint
+  if (resolutionStatus === "pending") {
+    throw new Error("PENDING is not a valid resolution action.")
+  }
+
   await checkDatasetAdmin(datasetId, currentUserId, userInfo)
 
   const originalRequestEvent = await DatasetEvent.findOne({
@@ -437,15 +399,23 @@ export async function processContributorCitation(
   obj,
   {
     eventId,
-    status,
+    status: graphqlStatus,
   }: {
     eventId: string
-    status: "accepted" | "denied"
+    status: "ACCEPTED" | "DENIED"
   },
   { user, userInfo }: { user: string; userInfo: { admin?: boolean } },
 ) {
   if (!user) throw new Error("Authentication required.")
 
+  const status = toDbStatus(graphqlStatus)
+
+  // Note that this is technically possible with hand-crafted GraphQL
+  // Separating types in the schema will enforce this at the endpoint
+  if (status === "pending") {
+    throw new Error("PENDING is not a valid resolution action.")
+  }
+
   const citationEvent = await DatasetEvent.findOne({ id: eventId })
 
   if (!citationEvent || citationEvent.event.type !== "contributorCitation") {

package/src/graphql/resolvers/draft.ts

@@ -5,7 +5,7 @@ import { description } from "./description.js"
 import { readme } from "./readme.js"
 import { getDraftRevision } from "../../datalad/draft.js"
 import { checkDatasetWrite } from "../permissions.js"
-import { getFiles } from "../../datalad/files"
+import { getFiles, getFilesRecursive } from "../../datalad/files"
 import { filterRemovedAnnexObjects } from "../utils/file.js"
 import { validation } from "./validation"
 import FileCheck from "../../models/fileCheck"
@@ -14,7 +14,10 @@ import { contributors } from "../../datalad/contributors"
 // A draft must have a dataset parent
 export const draftFiles = async (dataset, args, { userInfo }) => {
   const hexsha = await getDraftRevision(dataset.id)
-  const files = await getFiles(dataset.id, args.tree || hexsha)
+  const treeish = args.tree || hexsha
+  const files = args.recursive
+    ? await getFilesRecursive(dataset.id, treeish)
+    : await getFiles(dataset.id, treeish)
   return filterRemovedAnnexObjects(dataset.id, userInfo)(files)
 }
 

package/src/graphql/resolvers/holdDeletion.ts

@@ -0,0 +1,21 @@
+import Dataset from "../../models/dataset"
+
+/**
+ * Toggle the holdDeletion flag on a dataset to prevent automated deletion.
+ * Requires site admin access.
+ */
+export async function holdDeletion(
+  _obj: Record<string, unknown>,
+  { datasetId, hold }: { datasetId: string; hold: boolean },
+  { userInfo }: { userInfo: { admin: boolean } },
+): Promise<boolean> {
+  if (userInfo?.admin && datasetId.length === 8 && datasetId.startsWith("ds")) {
+    try {
+      await Dataset.updateOne({ id: datasetId }, { holdDeletion: hold }).exec()
+      return true
+    } catch (_err) {
+      return false
+    }
+  }
+  return false
+}

package/src/graphql/resolvers/index.ts

@@ -7,6 +7,10 @@ import Draft from "./draft.js"
 import Snapshot from "./snapshots.js"
 import User from "./user.js"
 import Comment from "./comment.js"
+import {
+  DatasetEventDescriptionTypeResolvers,
+  DatasetEventTypeResolvers,
+} from "./datasetEvents"
 
 export default {
   // Scalars
@@ -22,4 +26,6 @@ export default {
   Draft,
   Snapshot,
   Comment,
+  DatasetEvent: DatasetEventTypeResolvers,
+  DatasetEventDescription: DatasetEventDescriptionTypeResolvers,
 }

package/src/graphql/resolvers/mutation.ts

@@ -53,6 +53,7 @@ import {
 } from "./datasetEvents"
 import { createGitEvent } from "./gitEvents"
 import { fsckDataset, updateFileCheck } from "./fileCheck"
+import { holdDeletion } from "./holdDeletion"
 import { updateContributors } from "../../datalad/contributors"
 import { updateWorkerTask } from "./worker"
 
@@ -92,6 +93,7 @@ const Mutation = {
   cacheClear,
   revalidate,
   fsckDataset,
+  holdDeletion,
   prepareRepoAccess,
   reexportRemotes,
   resetDraft,

package/src/graphql/resolvers/response-status.ts

@@ -0,0 +1,43 @@
+/**
+ * Case mapping between the DB representation of resolutionStatus
+ * (lowercase: "pending" | "accepted" | "denied") and the GraphQL
+ * SDL enum ResponseStatusType (uppercase: "PENDING" | "ACCEPTED" | "DENIED").
+ *
+ * The DB layer enforces lowercase via Mongoose enum at
+ * packages/openneuro-server/src/models/datasetEvents.ts. These helpers mediate
+ * between that persisted representation and the typed GraphQL surface.
+ */
+
+export type DbStatus = "pending" | "accepted" | "denied"
+export type GraphqlStatus = "PENDING" | "ACCEPTED" | "DENIED"
+
+const DB_TO_GRAPHQL: Record<DbStatus, GraphqlStatus> = {
+  pending: "PENDING",
+  accepted: "ACCEPTED",
+  denied: "DENIED",
+}
+
+const GRAPHQL_TO_DB: Record<GraphqlStatus, DbStatus> = {
+  PENDING: "pending",
+  ACCEPTED: "accepted",
+  DENIED: "denied",
+}
+
+export function toGraphqlStatus(
+  value: DbStatus | null | undefined,
+): GraphqlStatus | null {
+  if (value === null || value === undefined) return null
+  const mapped = DB_TO_GRAPHQL[value]
+  if (!mapped) {
+    throw new Error(`toGraphqlStatus: unrecognized DB status value '${value}'`)
+  }
+  return mapped
+}
+
+export function toDbStatus(value: GraphqlStatus): DbStatus {
+  const mapped = GRAPHQL_TO_DB[value]
+  if (!mapped) {
+    throw new Error(`toDbStatus: unrecognized GraphQL status value '${value}'`)
+  }
+  return mapped
+}

package/src/graphql/resolvers/snapshots.ts

@@ -6,7 +6,7 @@ import { readme } from "./readme.js"
 import { description } from "./description.js"
 import { summary } from "./summary"
 import { issuesSnapshotStatus, snapshotIssues } from "./issues.js"
-import { getFiles } from "../../datalad/files"
+import { getFiles, getFilesRecursive } from "../../datalad/files"
 import Summary from "../../models/summary"
 import DatasetModel from "../../models/dataset"
 import { filterRemovedAnnexObjects } from "../utils/file"
@@ -14,7 +14,6 @@ import DeprecatedSnapshot from "../../models/deprecatedSnapshot"
 import { redis } from "../../libs/redis"
 import CacheItem, { CacheType } from "../../cache/item"
 import { normalizeDOI } from "../../libs/doi/normalize"
-import { downloadFiles } from "../../datalad/snapshots"
 import { snapshotValidation } from "./validation"
 import { advancedDatasetSearchConnection } from "./dataset-search"
 import { contributors } from "../../datalad/contributors"
@@ -34,10 +33,14 @@ export const snapshot = (obj, { datasetId, tag }, context) => {
         description: () => description(snapshot),
         readme: () => readme(snapshot),
         summary: () => summary({ id: datasetId, revision: snapshot.hexsha }),
-        files: ({ tree }) =>
-          getFiles(datasetId, tree || snapshot.hexsha).then(
+        files: ({ tree, recursive }) => {
+          const filesPromise = recursive
+            ? getFilesRecursive(datasetId, tree || snapshot.hexsha)
+            : getFiles(datasetId, tree || snapshot.hexsha)
+          return filesPromise.then(
             filterRemovedAnnexObjects(datasetId, context.userInfo),
-          ),
+          )
+        },
         size: () =>
           Summary.findOne({ datasetId: datasetId, id: snapshot.hexsha })
             .exec()
@@ -45,7 +48,6 @@ export const snapshot = (obj, { datasetId, tag }, context) => {
         deprecated: () => deprecated({ datasetId, tag }),
         related: () => related(datasetId),
         onBrainlife: () => onBrainlife(snapshot),
-        downloadFiles: () => downloadFiles(datasetId, tag),
       }))
     },
   )
@@ -140,17 +142,7 @@ export const undoDeprecateSnapshot = async (
 
 /** Query used to run a search for NIH datasets */
 const brainInitiativeQuery = {
-  "bool": {
-    "filter": [
-      {
-        "match": {
-          "brainInitiative": {
-            "query": "true",
-          },
-        },
-      },
-    ],
-  },
+  brainInitiative: true,
 }
 
 export const participantCount = (obj, { modality }) => {
@@ -178,7 +170,6 @@ export const participantCount = (obj, { modality }) => {
           query: brainInitiativeQuery,
           datasetType: "All Public",
           datasetStatus: "",
-          sortBy: "",
           after,
           first: 100,
         }, { user: null, userInfo: {} })

package/src/graphql/resolvers/summary.ts

@@ -1,3 +1,4 @@
+import { getDraftRevision } from "../../datalad/draft"
 import Summary from "../../models/summary"
 import type { SummaryDocument } from "../../models/summary"
 
@@ -51,3 +52,19 @@ export const updateSummary = (obj, args) => {
     .exec()
     .then(() => args.summary)
 }
+
+/**
+ * Get the primary modality for a dataset from the validator summary.
+ * Returns undefined if no summary is available.
+ */
+export async function getPrimaryModality(
+  datasetId: string,
+): Promise<string | undefined> {
+  try {
+    const revision = await getDraftRevision(datasetId)
+    const result = await summary({ id: datasetId, revision })
+    return result?.primaryModality || undefined
+  } catch {
+    return undefined
+  }
+}

package/src/graphql/schema.ts

@@ -215,8 +215,8 @@ export const typeDefs = `
       datasetId: ID!
       targetUserId: ID!
       requestId: ID!
-      resolutionStatus: String!
-      reason: String 
+      resolutionStatus: ResponseStatusType!
+      reason: String
     ): DatasetEvent
     # Create or update a fileCheck document
     updateFileCheck(
@@ -239,8 +239,10 @@ export const typeDefs = `
     ): DatasetEvent
     processContributorCitation(
       eventId: ID!
-      status: String!
+      status: ResponseStatusType!
     ): DatasetEvent
+    # Hold or release automated deletion for a dataset
+    holdDeletion(datasetId: ID!, hold: Boolean!): Boolean
     # Update worker task queue status
     updateWorkerTask(
       id: ID!,
@@ -267,6 +269,45 @@ export const typeDefs = `
     url: String!
   }
 
+  # Sort options for advanced dataset search
+  enum SearchSortOption {
+    relevance
+    newest
+    oldest
+    activity
+    name_asc
+    name_desc
+    last_updated
+  }
+
+  # Search input for advanced dataset search
+  input DatasetSearchInput {
+    keywords: [String]
+    modality: String
+    ageRange: [Int]
+    subjectCountRange: [Int]
+    diagnosis: String
+    tasks: [String]
+    authors: [String]
+    sex: String
+    dateRange: String
+    species: String
+    studyStructure: String
+    studyDomains: [String]
+    bidsDatasetType: String
+    brainInitiative: Boolean
+    bodyParts: [String]
+    scannerManufacturers: [String]
+    scannerManufacturersModelNames: [String]
+    tracerNames: [String]
+    tracerRadionuclides: [String]
+    sortBy: SearchSortOption
+    "Filter datasets by a specific user's permissions"
+    userId: String
+    "Filter to only public datasets"
+    publicOnly: Boolean
+  }
+
   input DeleteFile {
     path: String!
     filename: String
@@ -323,7 +364,7 @@ export const typeDefs = `
 
   input SubjectMetadataInput {
     participantId: String!
-    age: Int
+    age: Float
     sex: String
     group: String
   }
@@ -355,7 +396,7 @@ export const typeDefs = `
     openneuroPaperDOI: String
     seniorAuthor: String
     adminUsers: [String]
-    ages: [Int]
+    ages: [Float]
     modalities: [String]
     grantFunderName: String
     grantIdentifier: String
@@ -488,6 +529,8 @@ export const typeDefs = `
     brainInitiative: Boolean
     # Log of events associated with this dataset
     events: [DatasetEvent]
+    # Hold automated deletion for this dataset
+    holdDeletion: Boolean
   }
 
   type DatasetDerivatives {
@@ -581,7 +624,7 @@ export const typeDefs = `
     # Validator issues (schema validator)
     validation: DatasetValidation
     # Committed files in the working tree
-    files(tree: String): [DatasetFile]
+    files(tree: String, recursive: Boolean): [DatasetFile]
     # dataset_description.json fields
     description: Description
     # Dataset README
@@ -616,7 +659,7 @@ export const typeDefs = `
     # Validator issues (schema validator)
     validation: DatasetValidation
     # Snapshot files
-    files(tree: String): [DatasetFile]
+    files(tree: String, recursive: Boolean): [DatasetFile]
     # dataset_description.json fields
     description: Description
     # Snapshot usage and download statistics
@@ -633,8 +676,6 @@ export const typeDefs = `
     onBrainlife: Boolean @cacheControl(maxAge: 10080, scope: PUBLIC)
     # Total size in bytes of this snapshot
     size: BigInt
-    # Single list of files to download this snapshot (only available on snapshots)
-    downloadFiles: [DatasetFile]
     # Contributors list from datacite.yml
     contributors: [Contributor]
   }
@@ -784,7 +825,7 @@ export const typeDefs = `
 
   type SubjectMetadata {
     participantId: String!
-    age: Int
+    age: Float
     sex: String
     group: String
   }
@@ -871,7 +912,6 @@ export const typeDefs = `
   # File metadata and link to contents
   type DatasetFile {
     id: ID!
-    key: String
     filename: String!
     size: BigInt
     annexed: Boolean
@@ -934,7 +974,7 @@ export const typeDefs = `
     openneuroPaperDOI: String
     seniorAuthor: String
     adminUsers: [String]
-    ages: [Int]
+    ages: [Float]
     modalities: [String]
     grantFunderName: String
     grantIdentifier: String
@@ -975,7 +1015,7 @@ export const typeDefs = `
     requestId: ID
     reason: String
     datasetId: ID
-    resolutionStatus: String
+    resolutionStatus: ResponseStatusType
     contributorData: Contributor
   }
 
@@ -997,7 +1037,7 @@ export const typeDefs = `
     datasetId: ID
     # User's notification status event
     notificationStatus: UserNotificationStatus
-    responseStatus: String 
+    responseStatus: ResponseStatusType
     hasBeenRespondedTo: Boolean
   }
 

package/src/handlers/datalad.ts

@@ -86,7 +86,11 @@ export const getFile = async (req, res) => {
  */
 export const getObject = (req, res) => {
   const { datasetId, key } = req.params
+  const { filename } = req.query
   const worker = getDatasetWorker(datasetId)
+  if (req.query?.filename) {
+    res.set("Content-Disposition", `attachment; filename=${filename}`)
+  }
   // Backend depends on git object or git-annex key
   if (key.length === 40) {
     const uri = `${worker}/datasets/${datasetId}/objects/${key}`

package/src/handlers/doi.ts

@@ -1,44 +1,43 @@
 import config from "../config"
-import doi from "../libs/doi"
+import { createDraftDoi } from "../libs/doi"
+import { assembleMetadata } from "../libs/doi/metadata"
 import Doi from "../models/doi"
 import Snapshot from "../models/snapshot"
 
 export async function createSnapshotDoi(req, res) {
-  let doiRes = null
   if (!config.doi.username || !config.doi.password) {
-    return res.send({ doiRes: null })
+    return res.send({ doi: null })
   }
   const datasetId = req.params.datasetId
   const snapshotId = req.params.snapshotId
-  const oldDesc = req.body
-  const doiExists = await Doi.findOne({
-    datasetId: datasetId,
-    snapshotId: snapshotId,
-  })
+
+  // Return existing DOI if already registered
+  const doiExists = await Doi.findOne({ datasetId, snapshotId })
   if (doiExists) {
-    doiRes = doiExists.doi
-    return res.send({ doi: doiRes })
-  } else {
-    const snapExists = Snapshot.findOne({
-      datasetId: datasetId,
-      tag: snapshotId,
-    }).exec()
-    if (!snapExists) {
-      return
-    }
-    await doi
-      .registerSnapshotDoi(datasetId, snapshotId, oldDesc)
-      .then((doiRes) => {
-        if (doiRes) {
-          Doi.updateOne(
-            { datasetId: datasetId, snapshotId: snapshotId },
-            { $set: { doi: doiRes } },
-            { upsert: true },
-          )
-          return res.send({ doi: doiRes })
-        }
-        return res.send({ doiRes: null })
-      })
+    return res.send({ doi: doiExists.doi })
+  }
+
+  const snapExists = await Snapshot.findOne({
+    datasetId,
+    tag: snapshotId,
+  }).exec()
+  if (!snapExists) {
+    return res.status(404).send({ error: "Snapshot not found" })
+  }
+
+  try {
+    const attributes = await assembleMetadata(datasetId, snapshotId)
+    const doi = await createDraftDoi(attributes)
+
+    await Doi.updateOne(
+      { datasetId, snapshotId },
+      { $set: { doi, state: "draft" } },
+      { upsert: true },
+    )
+
+    return res.send({ doi })
+  } catch (err) {
+    return res.status(500).send({ error: err.message })
   }
 }
 
@@ -47,11 +46,8 @@ export async function getDoi(req, res) {
   const datasetId = req.params.datasetId
   const snapshotId = req.params.snapshotId
   const doi = await Doi.findOne(
-    {
-      datasetId: datasetId,
-      snapshotId: snapshotId,
-    },
-    "doi",
+    { datasetId, snapshotId },
+    "doi state",
   ).exec()
   return res.send(doi)
 }