@openneuro/server 4.20.5 → 4.20.6-alpha.2

package/src/graphql/resolvers/permissions.ts

@@ -1,8 +1,7 @@
-import User, { UserDocument } from '../../models/user'
-import Permission, { PermissionDocument } from '../../models/permission'
-import { checkDatasetAdmin } from '../permissions'
-import { user } from './user'
-import pubsub from '../pubsub.js'
+import User, { UserDocument } from "../../models/user"
+import Permission, { PermissionDocument } from "../../models/permission"
+import { checkDatasetAdmin } from "../permissions"
+import { user } from "./user"
 
 interface DatasetPermission {
   id: string
@@ -14,16 +13,15 @@ export async function permissions(ds): Promise<DatasetPermission> {
   return {
     id: ds.id,
     userPermissions: permissions.map(
-      userPermission =>
-        ({
-          ...userPermission.toJSON(),
-          user: user(ds, { id: userPermission.userId }),
-        } as PermissionDocument & { user: Promise<UserDocument> }),
+      (userPermission) => ({
+        ...userPermission.toJSON(),
+        user: user(ds, { id: userPermission.userId }),
+      } as PermissionDocument & { user: Promise<UserDocument> }),
     ),
   }
 }
 
-const publishPermissions = async datasetId => {
+const publishPermissions = async (datasetId) => {
   // Create permissionsUpdated object with DatasetPermissions in Dataset
   // and resolve all promises before publishing
   const ds = { id: datasetId }
@@ -33,17 +31,13 @@ const publishPermissions = async datasetId => {
     permissions: {
       id,
       userPermissions: await Promise.all(
-        userPermissions.map(async userPermission => ({
+        userPermissions.map(async (userPermission) => ({
           ...userPermission,
           user: await user(ds, { id: userPermission.userId }),
         })),
       ),
     },
   }
-  pubsub.publish('permissionsUpdated', {
-    datasetId,
-    permissionsUpdated,
-  })
 }
 
 /**
@@ -53,14 +47,14 @@ export const updatePermissions = async (obj, args, { user, userInfo }) => {
   await checkDatasetAdmin(args.datasetId, user, userInfo)
   // get all users the the email specified by permissions arg
   const users = await User.find({ email: args.userEmail })
-    .collation({ locale: 'en', strength: 2 })
+    .collation({ locale: "en", strength: 2 })
     .exec()
 
   if (!users.length) {
-    throw new Error('A user with that email address does not exist')
+    throw new Error("A user with that email address does not exist")
   }
 
-  const userPromises = users.map(user => {
+  const userPromises = users.map((user) => {
     return new Promise<void>((resolve, reject) => {
       Permission.updateOne(
         {
@@ -76,11 +70,11 @@ export const updatePermissions = async (obj, args, { user, userInfo }) => {
       )
         .exec()
         .then(() => resolve())
-        .catch(err => reject(err))
+        .catch((err) => reject(err))
     })
   })
   return Promise.all(userPromises).then(() =>
-    publishPermissions(args.datasetId),
+    publishPermissions(args.datasetId)
   )
 }
 

package/src/graphql/resolvers/publish.ts

@@ -0,0 +1,17 @@
+import config from "../../config"
+import request from "superagent"
+import { updatePublic } from "../../datalad/dataset"
+import { checkDatasetWrite } from "../permissions.js"
+import { generateDataladCookie } from "../../libs/authentication/jwt"
+import { getDatasetWorker } from "../../libs/datalad-service"
+
+export const publishDataset = (obj, { datasetId }, { user, userInfo }) => {
+  return checkDatasetWrite(datasetId, user, userInfo).then(async () => {
+    await updatePublic(datasetId, true)
+    const uri = `${getDatasetWorker(datasetId)}/datasets/${datasetId}/publish`
+    return await request
+      .post(uri)
+      .set("Cookie", generateDataladCookie(config)(userInfo))
+      .then(() => true)
+  })
+}

package/src/graphql/resolvers/query.ts

@@ -0,0 +1,21 @@
+/**
+ * Top level query
+ */
+import { dataset, datasets } from "./dataset.js"
+import { participantCount, snapshot } from "./snapshots.js"
+import { user, users } from "./user.js"
+import { flaggedFiles } from "./flaggedFiles"
+import { publicMetadata } from "./metadata"
+
+const Query = {
+  dataset,
+  datasets,
+  user,
+  users,
+  snapshot,
+  participantCount,
+  flaggedFiles,
+  publicMetadata,
+}
+
+export default Query

package/src/graphql/resolvers/{readme.js → readme.ts}

@@ -2,9 +2,9 @@
  * Resolver implementation for README files
  * This stub is here in case draft.readme or snapshot.readme needs future extension
  */
-import { setReadme } from '../../datalad/readme.js'
-import { checkDatasetWrite } from '../permissions.js'
-export { readme } from '../../datalad/readme.js'
+import { setReadme } from "../../datalad/readme"
+import { checkDatasetWrite } from "../permissions"
+export { readme } from "../../datalad/readme"
 
 export const updateReadme = (obj, { datasetId, value }, { user, userInfo }) => {
   return checkDatasetWrite(datasetId, user, userInfo).then(() => {

package/src/graphql/resolvers/{reexporter.js → reexporter.ts}

@@ -1,8 +1,8 @@
 /**
  * Resolver for rerunning remote exports.
  */
-import { checkAdmin } from '../permissions'
-import { runReexporter } from '../../datalad/reexporter'
+import { checkAdmin } from "../permissions"
+import { runReexporter } from "../../datalad/reexporter"
 
 export const reexportRemotes = async (
   obj,

package/src/graphql/resolvers/relation.ts

@@ -1,6 +1,6 @@
-import Dataset from '../../models/dataset'
-import { checkDatasetAdmin } from '../permissions'
-import { DOIPattern } from '../../libs/doi/normalize'
+import Dataset from "../../models/dataset"
+import { checkDatasetAdmin } from "../permissions"
+import { DOIPattern } from "../../libs/doi/normalize"
 
 export const createRelation = async (
   obj,
@@ -9,9 +9,9 @@ export const createRelation = async (
 ) => {
   await checkDatasetAdmin(datasetId, user, userInfo)
   // Validate the right DOI format
-  if (!doi.startsWith('doi:') || !doi.slice(4).match(DOIPattern)) {
+  if (!doi.startsWith("doi:") || !doi.slice(4).match(DOIPattern)) {
     throw new Error(
-      'DOI format must follow BIDS recommended format (see https://bids-specification.readthedocs.io/en/stable/02-common-principles.html#uniform-resource-indicator)',
+      "DOI format must follow BIDS recommended format (see https://bids-specification.readthedocs.io/en/stable/02-common-principles.html#uniform-resource-indicator)",
     )
   }
   const dataset = await Dataset.findOneAndUpdate(

package/src/graphql/resolvers/{reset.js → reset.ts}

@@ -1,5 +1,5 @@
-import { checkDatasetWrite } from '../permissions'
-import { resetDraft as resetDraftTask } from '../../datalad/draft'
+import { checkDatasetWrite } from "../permissions"
+import { resetDraft as resetDraftTask } from "../../datalad/draft"
 
 /**
  * Mutation to move the draft HEAD reference forward or backward

package/src/graphql/resolvers/reviewer.ts

@@ -1,7 +1,7 @@
-import config from '../../config'
-import Reviewer from '../../models/reviewer'
-import { checkDatasetAdmin } from '../permissions.js'
-import { generateReviewerToken } from '../../libs/authentication/jwt'
+import config from "../../config"
+import Reviewer from "../../models/reviewer"
+import { checkDatasetAdmin } from "../permissions.js"
+import { generateReviewerToken } from "../../libs/authentication/jwt"
 
 /**
  * Create an anonymous read-only access key

package/src/graphql/resolvers/{snapshots.js → snapshots.ts}

@@ -1,30 +1,30 @@
-import * as datalad from '../../datalad/snapshots.js'
-import { dataset, analytics, snapshotCreationComparison } from './dataset.js'
-import { onBrainlife } from './brainlife'
-import { checkDatasetRead, checkDatasetWrite } from '../permissions.js'
-import { readme } from './readme.js'
-import { description } from './description.js'
-import { summary } from './summary'
-import { snapshotIssues } from './issues.js'
-import { getFiles } from '../../datalad/files'
-import Summary from '../../models/summary'
-import DatasetModel from '../../models/dataset'
-import { filterRemovedAnnexObjects } from '../utils/file.js'
-import DeprecatedSnapshot from '../../models/deprecatedSnapshot'
-import { redis } from '../../libs/redis'
-import CacheItem, { CacheType } from '../../cache/item'
-import { normalizeDOI } from '../../libs/doi/normalize'
-import { getDraftHead } from '../../datalad/dataset'
-import { downloadFiles } from '../../datalad/snapshots'
+import * as datalad from "../../datalad/snapshots"
+import { analytics, dataset, snapshotCreationComparison } from "./dataset.js"
+import { onBrainlife } from "./brainlife"
+import { checkDatasetRead, checkDatasetWrite } from "../permissions"
+import { readme } from "./readme.js"
+import { description } from "./description.js"
+import { summary } from "./summary"
+import { snapshotIssues } from "./issues.js"
+import { getFiles } from "../../datalad/files"
+import Summary from "../../models/summary"
+import DatasetModel from "../../models/dataset"
+import { filterRemovedAnnexObjects } from "../utils/file"
+import DeprecatedSnapshot from "../../models/deprecatedSnapshot"
+import { redis } from "../../libs/redis"
+import CacheItem, { CacheType } from "../../cache/item"
+import { normalizeDOI } from "../../libs/doi/normalize"
+import { getDraftHead } from "../../datalad/dataset"
+import { downloadFiles } from "../../datalad/snapshots"
 
-export const snapshots = obj => {
+export const snapshots = (obj) => {
   return datalad.getSnapshots(obj.id)
 }
 
 export const snapshot = (obj, { datasetId, tag }, context) => {
   return checkDatasetRead(datasetId, context.user, context.userInfo).then(
     () => {
-      return datalad.getSnapshot(datasetId, tag).then(snapshot => ({
+      return datalad.getSnapshot(datasetId, tag).then((snapshot) => ({
         ...snapshot,
         dataset: () => dataset(snapshot, { id: datasetId }, context),
         description: () => description(snapshot),
@@ -37,7 +37,7 @@ export const snapshot = (obj, { datasetId, tag }, context) => {
         size: () =>
           Summary.findOne({ datasetId: datasetId, id: snapshot.hexsha })
             .exec()
-            .then(res => res?.toObject()?.size),
+            .then((res) => res?.toObject()?.size),
         deprecated: () => deprecated({ datasetId, tag }),
         related: () => related(datasetId),
         onBrainlife: () => onBrainlife(snapshot),
@@ -56,23 +56,23 @@ export const deprecated = ({ datasetId, tag }) => {
  * Search dataset metadeta for related objects and return an array
  * @param {string} datasetId
  */
-export const related = async datasetId => {
+export const related = async (datasetId) => {
   const dataset = await DatasetModel.findOne({ id: datasetId }).lean().exec()
   return dataset.related
 }
 
-export const matchKnownObjects = desc => {
+export const matchKnownObjects = (desc) => {
   if (desc?.ReferencesAndLinks) {
     const objects = []
     for (const item of desc.ReferencesAndLinks) {
       try {
         const rawDOI = normalizeDOI(item)
         // NIMH Data Archive (NDA) 10.15154
-        if (rawDOI.startsWith('10.15154')) {
+        if (rawDOI.startsWith("10.15154")) {
           objects.push({
             id: rawDOI,
-            source: 'NDA',
-            type: 'dataset',
+            source: "NDA",
+            type: "dataset",
           })
         } else {
           objects.push({ id: rawDOI })
@@ -138,24 +138,24 @@ export const participantCount = (obj, { modality }) => {
   const cache = new CacheItem(
     redis,
     CacheType.participantCount,
-    [modality || 'all'],
+    [modality || "all"],
     3600,
   )
   return cache.get(async () => {
     const queryHasSubjects = {
-      'summary.subjects': {
+      "summary.subjects": {
         $exists: true,
       },
     }
     const matchQuery = modality
       ? {
-          $and: [
-            queryHasSubjects,
-            {
-              'summary.modalities.0': modality,
-            },
-          ],
-        }
+        $and: [
+          queryHasSubjects,
+          {
+            "summary.modalities.0": modality,
+          },
+        ],
+      }
       : queryHasSubjects
     const aggregateResult = await DatasetModel.aggregate([
       {
@@ -165,24 +165,24 @@ export const participantCount = (obj, { modality }) => {
       },
       {
         $lookup: {
-          from: 'snapshots',
-          localField: 'id',
-          foreignField: 'datasetId',
-          as: 'snapshots',
+          from: "snapshots",
+          localField: "id",
+          foreignField: "datasetId",
+          as: "snapshots",
         },
       },
       {
         $project: {
-          id: '$id',
-          hexsha: { $arrayElemAt: ['$snapshots.hexsha', -1] },
+          id: "$id",
+          hexsha: { $arrayElemAt: ["$snapshots.hexsha", -1] },
         },
       },
       {
         $lookup: {
-          from: 'summaries',
-          localField: 'hexsha',
-          foreignField: 'id',
-          as: 'summary',
+          from: "summaries",
+          localField: "hexsha",
+          foreignField: "id",
+          as: "summary",
         },
       },
       {
@@ -192,7 +192,7 @@ export const participantCount = (obj, { modality }) => {
         $group: {
           _id: null,
           participantCount: {
-            $sum: { $size: { $arrayElemAt: ['$summary.subjects', 0] } },
+            $sum: { $size: { $arrayElemAt: ["$summary.subjects", 0] } },
           },
         },
       },
@@ -206,7 +206,7 @@ export const participantCount = (obj, { modality }) => {
  * Select the most recent snapshot from an array of snapshots
  * @param {*} snapshots Array of snapshot objects from datalad.getSnapshots
  */
-export const filterLatestSnapshot = snapshots => {
+export const filterLatestSnapshot = (snapshots) => {
   if (snapshots.length) {
     const sortedSnapshots = Array.prototype.sort.call(
       snapshots,
@@ -256,8 +256,8 @@ export const deleteSnapshot = (obj, { datasetId, tag }, { user, userInfo }) => {
 }
 
 const Snapshot = {
-  analytics: snapshot => analytics(snapshot),
-  issues: snapshot => snapshotIssues(snapshot),
+  analytics: (snapshot) => analytics(snapshot),
+  issues: (snapshot) => snapshotIssues(snapshot),
 }
 
 export default Snapshot

package/src/graphql/resolvers/{stars.js → stars.ts}

@@ -1,4 +1,4 @@
-import Star from '../../models/stars'
+import Star from "../../models/stars"
 
 export const starDataset = async (obj, { datasetId }, { user }) => {
   const star = await Star.findOne({ datasetId, userId: user }).exec()

package/src/graphql/resolvers/summary.ts

@@ -1,5 +1,5 @@
-import Summary, { SummaryDocument } from '../../models/summary'
-import { datasetType } from './datasetType'
+import Summary, { SummaryDocument } from "../../models/summary"
+import { datasetType } from "./datasetType"
 
 /**
  * Summary resolver
@@ -11,7 +11,7 @@ export async function summary(dataset): Promise<Partial<SummaryDocument>> {
       datasetId: dataset.id,
       // Match if we have no validatorMetadata or the correct 'legacy' / 'schema' value if we do
       $or: [
-        { 'validatorMetadata.validator': await datasetType(dataset) },
+        { "validatorMetadata.validator": await datasetType(dataset) },
         { validatorMetadata: { $exists: false } },
       ],
     }).exec()

package/src/graphql/resolvers/{upload.js → upload.ts}

@@ -1,8 +1,8 @@
-import Upload from '../../models/upload'
-import { checkDatasetWrite } from '../permissions.js'
-import { generateUploadToken } from '../../libs/authentication/jwt'
-import { finishUploadRequest } from '../../datalad/upload.js'
-import { getDatasetEndpoint } from '../../libs/datalad-service.js'
+import Upload from "../../models/upload"
+import { checkDatasetWrite } from "../permissions.js"
+import { generateUploadToken } from "../../libs/authentication/jwt"
+import { finishUploadRequest } from "../../datalad/upload.js"
+import { getDatasetEndpoint } from "../../libs/datalad-service.js"
 
 /**
  * Track initial state for a new upload

package/src/graphql/resolvers/{user.js → user.ts}

@@ -1,9 +1,7 @@
 /**
  * User resolvers
- *
- * These are passthroughs to SciTran until we have authentication working internally
  */
-import User from '../../models/user'
+import User from "../../models/user"
 
 export const user = (obj, { id }) => {
   return User.findOne({ id }).exec()
@@ -14,7 +12,7 @@ export const users = (obj, args, { userInfo }) => {
     return User.find().exec()
   } else {
     return Promise.reject(
-      new Error('You must be a site admin to retrieve users'),
+      new Error("You must be a site admin to retrieve users"),
     )
   }
 }
@@ -23,7 +21,7 @@ export const removeUser = (obj, { id }, { userInfo }) => {
   if (userInfo.admin) {
     return User.findByIdAndRemove(id).exec()
   } else {
-    return Promise.reject(new Error('You must be a site admin to remove users'))
+    return Promise.reject(new Error("You must be a site admin to remove users"))
   }
 }
 
@@ -32,7 +30,7 @@ export const setAdmin = (obj, { id, admin }, { userInfo }) => {
     return User.findOneAndUpdate({ id }, { admin }).exec()
   } else {
     return Promise.reject(
-      new Error('You must be a site admin to modify this value'),
+      new Error("You must be a site admin to modify this value"),
     )
   }
 }
@@ -41,22 +39,22 @@ export const setBlocked = (obj, { id, blocked }, { userInfo }) => {
   if (userInfo.admin) {
     return User.findOneAndUpdate({ id }, { blocked }).exec()
   } else {
-    return Promise.reject(new Error('You must be a site admin to block a user'))
+    return Promise.reject(new Error("You must be a site admin to block a user"))
   }
 }
 
 const UserResolvers = {
-  id: obj => obj.id,
-  provider: obj => obj.provider,
-  avatar: obj => obj.avatar,
-  orcid: obj => obj.orcid,
-  created: obj => obj.created,
-  modified: obj => obj.modified,
-  lastSeen: obj => obj.lastSeen,
-  email: obj => obj.email,
-  name: obj => obj.name,
-  admin: obj => obj.admin,
-  blocked: obj => obj.blocked,
+  id: (obj) => obj.id,
+  provider: (obj) => obj.provider,
+  avatar: (obj) => obj.avatar,
+  orcid: (obj) => obj.orcid,
+  created: (obj) => obj.created,
+  modified: (obj) => obj.modified,
+  lastSeen: (obj) => obj.lastSeen,
+  email: (obj) => obj.email,
+  name: (obj) => obj.name,
+  admin: (obj) => obj.admin,
+  blocked: (obj) => obj.blocked,
 }
 
 export default UserResolvers

package/src/graphql/resolvers/{validation.js → validation.ts}

@@ -1,9 +1,8 @@
-import config from '../../config'
-import { generateDataladCookie } from '../../libs/authentication/jwt'
-import { getDatasetWorker } from '../../libs/datalad-service'
-import Issue from '../../models/issue'
-import publishDraftUpdate from '../utils/publish-draft-update.js'
-import { redlock } from '../../libs/redis.js'
+import config from "../../config"
+import { generateDataladCookie } from "../../libs/authentication/jwt"
+import { getDatasetWorker } from "../../libs/datalad-service"
+import Issue from "../../models/issue"
+import { redlock } from "../../libs/redis"
 
 /**
  * Save issues data returned by the datalad service
@@ -23,16 +22,15 @@ export const updateValidation = (obj, args) => {
     },
   )
     .exec()
-    .then(() => {
-      publishDraftUpdate(args.validation.datasetId, args.validation.id)
-      return true
-    })
+    .then(() => true)
 }
 
 export const validationUrl = (datasetId, ref) => {
-  return `http://${getDatasetWorker(
-    datasetId,
-  )}/datasets/${datasetId}/validate/${ref}`
+  return `http://${
+    getDatasetWorker(
+      datasetId,
+    )
+  }/datasets/${datasetId}/validate/${ref}`
 }
 
 /**
@@ -47,7 +45,7 @@ export const revalidate = async (obj, { datasetId, ref }, { userInfo }) => {
     // Lock for five minutes to avoid stacking up multiple validation requests
     await redlock.lock(`openneuro:revalidate-lock:${datasetId}:${ref}`, 300000)
     const response = await fetch(validationUrl(datasetId, ref), {
-      method: 'POST',
+      method: "POST",
       body: JSON.stringify({}),
       headers: {
         cookie: generateDataladCookie(config)(userInfo),

package/src/graphql/{schema.js → schema.ts}

@@ -1,11 +1,10 @@
 // @ts-nocheck
-import { schemaComposer } from 'graphql-compose'
-import resolvers from './resolvers'
-import Subscription from './resolvers/subscriptions.js'
+import { schemaComposer } from "graphql-compose"
+import resolvers from "./resolvers"
 import {
-  datasetSearch,
   advancedDatasetSearch,
-} from './resolvers/dataset-search'
+  datasetSearch,
+} from "./resolvers/dataset-search"
 
 export const typeDefs = `
   scalar Date
@@ -818,7 +817,6 @@ export const typeDefs = `
 
 schemaComposer.addTypeDefs(typeDefs)
 schemaComposer.addResolveMethods(resolvers)
-schemaComposer.Subscription.addFields(Subscription)
 schemaComposer.Query.addFields(datasetSearch)
 schemaComposer.Query.addFields(advancedDatasetSearch)
 

package/src/graphql/utils/{file.js → file.ts}

@@ -1,7 +1,7 @@
-import BadAnnexObject from '../../models/badAnnexObject'
+import BadAnnexObject from "../../models/badAnnexObject"
 
 export const filterRemovedAnnexObjects =
-  (datasetId, userInfo) => async files => {
+  (datasetId, userInfo) => async (files) => {
     const removedAnnexObjectKeys = (
       await BadAnnexObject.find({ datasetId }).exec()
     ).map(({ annexKey }) => annexKey)

package/src/handlers/{comments.js → comments.ts}

@@ -1,11 +1,11 @@
 // @ts-nocheck
-import notifications from '../libs/notifications.js'
-import { format } from 'date-fns/format'
-import User from '../models/user'
-import Comment from '../models/comment'
-import MailgunIdentifier from '../models/mailgunIdentifier'
-import { ContentState, convertFromHTML, convertToRaw } from 'draft-js'
-import mongoose from 'mongoose'
+import notifications from "../libs/notifications.js"
+import { format } from "date-fns/format"
+import User from "../models/user"
+import Comment from "../models/comment"
+import MailgunIdentifier from "../models/mailgunIdentifier"
+import { ContentState, convertFromHTML, convertToRaw } from "draft-js"
+import mongoose from "mongoose"
 const ObjectID = mongoose.Schema.Types.ObjectId
 
 /**
@@ -15,7 +15,7 @@ const ObjectID = mongoose.Schema.Types.ObjectId
  * item that can be stored as if it came from
  * a client-side draft.js editor
  */
-const textToDraft = text => {
+const textToDraft = (text) => {
   return JSON.stringify(
     convertToRaw(ContentState.createFromBlockArray(convertFromHTML(text))),
   )
@@ -36,10 +36,10 @@ export async function reply(req, res, next) {
   const userId = req.params.userId
     ? decodeURIComponent(req.params.userId)
     : null
-  const text = textToDraft(req.body['stripped-text'])
-  const inReplyToRaw = req.body['In-Reply-To']
+  const text = textToDraft(req.body["stripped-text"])
+  const inReplyToRaw = req.body["In-Reply-To"]
   const inReplyTo = inReplyToRaw
-    ? inReplyToRaw.replace('<', '').replace('>', '')
+    ? inReplyToRaw.replace("<", "").replace(">", "")
     : null
   const messageId = inReplyTo
     ? await MailgunIdentifier.findOne({ messageId: inReplyTo }).exec()

package/src/handlers/{config.js → config.ts}

@@ -22,5 +22,5 @@ const config = {
 // Provide some environment variables to the client
 export const clientConfig = (req, res) => {
   const configScript = `window.OpenNeuroConfig = ${JSON.stringify(config)}`
-  res.type('text/javascript').send(configScript)
+  res.type("text/javascript").send(configScript)
 }