@openneuro/server 4.30.2 → 4.31.0

package/src/graphql/resolvers/brainInitiative.ts

@@ -0,0 +1,65 @@
+import { redis } from "../../libs/redis"
+import type { DatasetOrSnapshot } from "../../utils/datasetOrSnapshot"
+import { latestSnapshot } from "./snapshots"
+import { description } from "../../datalad/description"
+import Metadata from "../../models/metadata"
+import CacheItem, { CacheType } from "../../cache/item"
+import * as Sentry from "@sentry/node"
+import fundedAwards from "../../data/funded_awards.json"
+
+const brainInitiativeMatch = new RegExp("brain.initiative", "i")
+
+const brainInitiativeGrants = fundedAwards.map((award) =>
+  award.field_project_number.replace(/[^a-zA-Z0-9]/g, "")
+)
+
+/**
+ * Check for any Brain Initiative metadata
+ */
+export const brainInitiative = async (
+  dataset: DatasetOrSnapshot,
+  _,
+  context,
+): Promise<boolean> => {
+  const cache = new CacheItem(
+    redis,
+    CacheType.brainInitiative,
+    [dataset.id],
+    86400,
+  )
+  return await cache.get(async () => {
+    try {
+      const metadata = await Metadata.findOne({ datasetId: dataset.id })
+      if (metadata.grantFunderName.match(brainInitiativeMatch)) {
+        return true
+      } else {
+        // Fetch snapshot if metadata didn't match
+        const snapshot = await latestSnapshot(dataset, null, context)
+        const snapshotDescription = await description(snapshot)
+        for (const funding of snapshotDescription.Funding) {
+          if (funding.match(brainInitiativeMatch)) {
+            return true
+          }
+        }
+        // Check for grant ids too - filter to only alphanumeric to improve matching across format differences
+        const identifier = metadata.grantIdentifier.replace(/[^a-zA-Z0-9]/g, "")
+        for (const grant of brainInitiativeGrants) {
+          if (
+            identifier.includes(grant)
+          ) {
+            return true
+          }
+          for (const funding of snapshotDescription.Funding) {
+            if (funding.replace(/[^a-zA-Z0-9]/g, "").includes(grant)) {
+              return true
+            }
+          }
+        }
+      }
+      return false
+    } catch (_err) {
+      Sentry.captureException(_err)
+      return false
+    }
+  })
+}

package/src/graphql/resolvers/dataset.ts

@@ -19,6 +19,7 @@ import { reviewers } from "./reviewer"
 import { getDatasetWorker } from "../../libs/datalad-service"
 import { getFileName } from "../../datalad/files"
 import { onBrainlife } from "./brainlife"
+import { brainInitiative } from "./brainInitiative"
 import { derivatives } from "./derivatives"
 import { promiseTimeout } from "../../utils/promiseTimeout"
 import semver from "semver"
@@ -301,6 +302,7 @@ const Dataset = {
   history,
   worker,
   reviewers,
+  brainInitiative,
 }
 
 export default Dataset

package/src/graphql/resolvers/metadata.ts

@@ -1,5 +1,5 @@
 import Snapshot from "../../models/snapshot"
-import type { LeanDocument } from "mongoose"
+import type { FlattenMaps } from "mongoose"
 import DatasetModel from "../../models/dataset"
 import MetadataModel from "../../models/metadata"
 import type { MetadataDocument } from "../../models/metadata"
@@ -15,7 +15,7 @@ export const metadata = async (
   dataset,
   _,
   context,
-): Promise<LeanDocument<MetadataDocument>> => {
+): Promise<FlattenMaps<MetadataDocument>> => {
   const record = await MetadataModel.findOne({
     datasetId: dataset.id,
   }).lean()
@@ -73,11 +73,11 @@ export const addMetadata = async (obj, { datasetId, metadata }) => {
  */
 export async function publicMetadata(
   _obj,
-): Promise<LeanDocument<MetadataDocument>[]> {
+): Promise<FlattenMaps<MetadataDocument>[]> {
   const datasets = await DatasetModel.find({
     public: true,
   }).lean()
-  const dsMetadata: LeanDocument<MetadataDocument>[] = []
+  const dsMetadata: FlattenMaps<MetadataDocument>[] = []
   for (const ds of datasets) {
     dsMetadata.push(await metadata(ds, null, {}))
   }

package/src/graphql/resolvers/permissions.ts

@@ -18,7 +18,7 @@ export async function permissions(ds): Promise<DatasetPermission> {
       (userPermission) => ({
         ...userPermission.toJSON(),
         user: user(ds, { id: userPermission.userId }),
-      } as PermissionDocument & { user: Promise<UserDocument> }),
+      } as unknown as PermissionDocument & { user: Promise<UserDocument> }),
     ),
   }
 }

package/src/graphql/resolvers/user.ts

@@ -29,7 +29,7 @@ export const users = (obj, args, { userInfo }) => {
 
 export const removeUser = (obj, { id }, { userInfo }) => {
   if (userInfo.admin) {
-    return User.findByIdAndRemove(id).exec()
+    return User.findByIdAndDelete(id).exec()
   } else {
     return Promise.reject(new Error("You must be a site admin to remove users"))
   }

package/src/graphql/resolvers/validation.ts

@@ -22,7 +22,15 @@ export const validation = async (dataset, _, { userInfo }) => {
           { userInfo },
         )
       }
-      return data
+      // Return with errors and warning counts appended
+      return {
+        ...data.toObject(),
+        errors: data.issues.filter((issue) =>
+          issue.severity === "error"
+        ).length,
+        warnings:
+          data.issues.filter((issue) => issue.severity === "warning").length,
+      }
     })
 }
 
@@ -31,11 +39,18 @@ export const validation = async (dataset, _, { userInfo }) => {
  */
 export const snapshotValidation = async (snapshot) => {
   const datasetId = snapshot.id.split(":")[0]
-  return Validation.findOne({
+  const validation = await Validation.findOne({
     id: snapshot.hexsha,
     datasetId,
-  })
-    .exec()
+  }).exec()
+  // Return with errors and warning counts appended
+  return {
+    ...validation.toObject(),
+    errors:
+      validation.issues.filter((issue) => issue.severity === "error").length,
+    warnings:
+      validation.issues.filter((issue) => issue.severity === "warning").length,
+  }
 }
 
 export function validationSeveritySort(a, b) {

package/src/graphql/schema.ts

@@ -410,6 +410,8 @@ export const typeDefs = `
     worker: String
     # Anonymous reviewers for this dataset
     reviewers: [DatasetReviewer]
+    # Dataset belongs to Brain Initiative
+    brainInitiative: Boolean
   }
 
   type DatasetDerivatives {
@@ -475,8 +477,13 @@ export const typeDefs = `
     # Hash of the data validated
     id: String
     datasetId: String
+    # Issue objects returned by BIDS validator
     issues: [ValidatorIssue]
     codeMessages: [ValidatorCodeMessage]
+    # Count of errors
+    errors: Int
+    # Count of warnings
+    warnings: Int
   }
 
   # Ephemeral draft or working tree for a dataset

package/src/libs/authentication/migration.ts

@@ -0,0 +1,22 @@
+/** 
+ * Migration of accounts from previous providers (Google) to ORCID as primary authentication
+ * 
+ * Runs on successful oauth linking these accounts
+ * 
+ * Either Google -> ORCID (creates / updates ORCID account with the Google account and merges any data) 
+ * or ORCID + Google (merges Google account data into existing account)
+ */
+
+/**
+ * 
+ */
+function migrationOrcidToGoogle() {
+
+}
+
+/**
+ * 
+ */
+function migrationGoogleToOrcid() {
+
+}

package/src/models/subscription.ts

@@ -3,6 +3,7 @@ import type { Document } from "mongoose"
 const { Schema, model } = mongoose
 
 export interface SubscriptionDocument extends Document {
+  _id: string
   datasetId: string
   userId: string
 }

package/src/models/user.ts

@@ -4,6 +4,7 @@ import type { Document } from "mongoose"
 const { Schema, model } = mongoose
 
 export interface UserDocument extends Document {
+  _id: string
   id: string
   email: string
   name: string

package/tsconfig.json

@@ -9,9 +9,8 @@
     "module": "CommonJS"
   },
   "include": ["./src"],
-  "files": ["./src/lerna.json"],
+  "files": ["./src/lerna.json", "./src/data/funded_awards.json"],
   "references": [
-    { "path": "../openneuro-client" },
     { "path": "../openneuro-search" }
   ]
 }