@openneuro/server 4.20.5 → 4.20.6-alpha.3

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

@@ -1,28 +1,26 @@
-import * as datalad from '../../datalad/dataset.js'
-import pubsub from '../pubsub.js'
-import { removeDatasetSearchDocument } from '../../graphql/resolvers/dataset-search.js'
-import { snapshots, latestSnapshot } from './snapshots.js'
-import { description } from './description.js'
+import * as datalad from "../../datalad/dataset"
+import { removeDatasetSearchDocument } from "./dataset-search"
+import { latestSnapshot, snapshots } from "./snapshots"
+import { description } from "./description"
 import {
+  checkDatasetAdmin,
   checkDatasetRead,
   checkDatasetWrite,
-  checkDatasetAdmin,
-} from '../permissions'
-import { user } from './user.js'
-import { permissions } from './permissions'
-import { datasetComments } from './comment.js'
-import { metadata } from './metadata'
-import { history } from './history.js'
-import * as dataladAnalytics from '../../datalad/analytics.js'
-import DatasetModel from '../../models/dataset'
-import Deletion from '../../models/deletion'
-import { reviewers } from './reviewer'
-import { getDatasetWorker } from '../../libs/datalad-service.js'
-import { getDraftHead } from '../../datalad/dataset.js'
-import { getFileName } from '../../datalad/files'
-import { onBrainlife } from './brainlife'
-import { derivatives } from './derivatives'
-import semver from 'semver'
+} from "../permissions"
+import { user } from "./user"
+import { permissions } from "./permissions"
+import { datasetComments } from "./comment"
+import { metadata } from "./metadata"
+import { history } from "./history"
+import * as dataladAnalytics from "../../datalad/analytics"
+import DatasetModel from "../../models/dataset"
+import Deletion from "../../models/deletion"
+import { reviewers } from "./reviewer"
+import { getDatasetWorker } from "../../libs/datalad-service"
+import { getFileName } from "../../datalad/files"
+import { onBrainlife } from "./brainlife"
+import { derivatives } from "./derivatives"
+import semver from "semver"
 
 export const dataset = async (obj, { id }, { user, userInfo }) => {
   await checkDatasetRead(id, user, userInfo)
@@ -56,21 +54,21 @@ export const snapshotCreationComparison = (
  * Find the canonical name for a dataset from snapshots and drafts
  * @param {object} obj Dataset object (at least {id: "datasetId"})
  */
-export const datasetName = obj => {
-  return snapshots(obj).then(results => {
+export const datasetName = (obj) => {
+  return snapshots(obj).then((results) => {
     if (results && results.length) {
       // Return the latest snapshot name
       const sortedSnapshots = results.sort(snapshotCreationComparison)
       return description({
         id: obj.id,
         revision: sortedSnapshots[0].hexsha,
-      }).then(desc => desc.Name)
+      }).then((desc) => desc.Name)
     } else if (obj.revision) {
       // Return the draft name or null
       return description({
         id: obj.id,
         revision: obj.revision,
-      }).then(desc => desc.Name)
+      }).then((desc) => desc.Name)
     } else {
       return null
     }
@@ -81,9 +79,9 @@ export const datasetName = obj => {
  * Resolve the best dataset name and cache in mongodb
  * @param {string} datasetId
  */
-export const updateDatasetName = datasetId =>
-  datasetName({ id: datasetId }).then(name =>
-    DatasetModel.updateOne({ id: datasetId }, { $set: { name } }).exec(),
+export const updateDatasetName = (datasetId) =>
+  datasetName({ id: datasetId }).then((name) =>
+    DatasetModel.updateOne({ id: datasetId }, { $set: { name } }).exec()
   )
 
 /**
@@ -103,11 +101,11 @@ export const createDataset = (
       })
     } else {
       throw new Error(
-        'New dataset must be defaced or have participant consent.',
+        "New dataset must be defaced or have participant consent.",
       )
     }
   } else {
-    throw new Error('You must be logged in to create a dataset.')
+    throw new Error("You must be logged in to create a dataset.")
   }
 }
 
@@ -134,10 +132,6 @@ export const deleteDataset = async (
     redirect,
     user: { _id: user },
   }).save()
-  await pubsub.publish('datasetDeleted', {
-    datasetId: id,
-    datasetDeleted: id,
-  })
   return deleted
 }
 
@@ -152,14 +146,6 @@ export const deleteFiles = async (
   try {
     await checkDatasetWrite(datasetId, user, userInfo)
     const deletedFiles = await datalad.deleteFiles(datasetId, files, userInfo)
-    pubsub.publish('filesUpdated', {
-      datasetId,
-      filesUpdated: {
-        action: 'DELETE',
-        payload: deletedFiles,
-      },
-    })
-
     return true
   } catch (err) {
     return false
@@ -223,7 +209,7 @@ export const updatePublic = (
 /**
  * Get analytics for a dataset or snapshot
  */
-export const analytics = async obj => {
+export const analytics = async (obj) => {
   // if the dataset field exists, the request is from a snapshot, and
   // we resolve the datasetId from the dataset snapshot field of context.
   // otherwise, just use the id field because the object is a dataset
@@ -249,7 +235,7 @@ export const trackAnalytics = (obj, { datasetId, tag, type }) => {
 /**
  * Get the star count for the dataset
  */
-export const stars = async obj => {
+export const stars = async (obj) => {
   const datasetId = obj && obj.dataset ? (await obj.dataset()).id : obj.id
   return datalad.getStars(datasetId)
 }
@@ -257,7 +243,7 @@ export const stars = async obj => {
 /**
  * Get the follower count for the dataset
  */
-export const followers = async obj => {
+export const followers = async (obj) => {
   const datasetId = obj && obj.dataset ? (await obj.dataset()).id : obj.id
   return datalad.getFollowers(datasetId)
 }
@@ -269,7 +255,7 @@ export const followers = async obj => {
  */
 export const following = (obj, _, { user }) =>
   user
-    ? datalad.getUserFollowed(obj.id, user).then(res => (res ? true : false))
+    ? datalad.getUserFollowed(obj.id, user).then((res) => (res ? true : false))
     : null
 
 /**
@@ -279,19 +265,19 @@ export const following = (obj, _, { user }) =>
  */
 export const starred = (obj, _, { user }) =>
   user
-    ? datalad.getUserStarred(obj.id, user).then(res => (res ? true : false))
+    ? datalad.getUserStarred(obj.id, user).then((res) => (res ? true : false))
     : null
 
-const worker = obj => getDatasetWorker(obj.id)
+const worker = (obj) => getDatasetWorker(obj.id)
 
 /**
  * Dataset object
  */
 const Dataset = {
-  uploader: ds => user(ds, { id: ds.uploader }),
-  draft: async obj => ({
+  uploader: (ds) => user(ds, { id: ds.uploader }),
+  draft: async (obj) => ({
     id: obj.id,
-    revision: await getDraftHead(obj.id),
+    revision: await datalad.getDraftHead(obj.id),
     modified: obj.modified,
   }),
   snapshots,

package/src/graphql/resolvers/datasetType.ts

@@ -1,6 +1,6 @@
-import { description } from './description.js'
+import { description } from "./description.js"
 
-export async function datasetType(dsOrSnapshot): Promise<'schema' | 'legacy'> {
+export async function datasetType(dsOrSnapshot): Promise<"schema" | "legacy"> {
   const dsDescription = await description(dsOrSnapshot)
-  return dsDescription.DatasetType === 'derivative' ? 'schema' : 'legacy'
+  return dsDescription.DatasetType === "derivative" ? "schema" : "legacy"
 }

package/src/graphql/resolvers/derivatives.ts

@@ -1,14 +1,14 @@
 import {
   DatasetOrSnapshot,
   getDatasetFromSnapshotId,
-} from '../../utils/datasetOrSnapshot'
-import config from '../../config'
+} from "../../utils/datasetOrSnapshot"
+import config from "../../config"
 
-const S3_BUCKET = 'openneuro-derivatives'
-const GITHUB_ORGANIZATION = 'OpenNeuroDerivatives'
+const S3_BUCKET = "openneuro-derivatives"
+const GITHUB_ORGANIZATION = "OpenNeuroDerivatives"
 
 // Available derivatives at this time
-type GitHubDerivative = 'mriqc' | 'fmriprep'
+type GitHubDerivative = "mriqc" | "fmriprep"
 
 /**
  * Test for a derivative on GitHub via API
@@ -49,7 +49,7 @@ export const githubDerivative = async (
   }
 }
 
-interface DatasetDerivatives {
+export interface DatasetDerivatives {
   name: string
   local: boolean
   s3Url: URL
@@ -80,17 +80,17 @@ export const derivatives = async (
   dataset: DatasetOrSnapshot,
 ): Promise<Array<DatasetDerivatives>> => {
   let datasetId
-  if ('tag' in dataset) {
+  if ("tag" in dataset) {
     datasetId = getDatasetFromSnapshotId(dataset.id)
   } else {
     datasetId = dataset.id
   }
   const available: Array<DatasetDerivatives> = []
-  if (await githubDerivative(datasetId, 'mriqc')) {
-    available.push(derivativeObject(datasetId, 'mriqc'))
+  if (await githubDerivative(datasetId, "mriqc")) {
+    available.push(derivativeObject(datasetId, "mriqc"))
   }
-  if (await githubDerivative(datasetId, 'fmriprep')) {
-    available.push(derivativeObject(datasetId, 'fmriprep'))
+  if (await githubDerivative(datasetId, "fmriprep")) {
+    available.push(derivativeObject(datasetId, "fmriprep"))
   }
   return available
 }

package/src/graphql/resolvers/description.ts

@@ -0,0 +1,18 @@
+/**
+ * Resolver implementation for dataset_description.json
+ */
+import { setDescription } from "../../datalad/description"
+import { checkDatasetWrite } from "../permissions"
+export { description } from "../../datalad/description"
+
+export const updateDescription = (
+  obj,
+  { datasetId, field, value },
+  { user, userInfo },
+) => {
+  return checkDatasetWrite(datasetId, user, userInfo)
+    .then(() => setDescription(datasetId, userInfo, { [field]: value }))
+    .then((description) => description)
+}
+
+export const updateDescriptionList = updateDescription

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

@@ -1,12 +1,12 @@
-import Summary from '../../models/summary'
-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 { checkDatasetWrite } from '../permissions.js'
-import { getFiles } from '../../datalad/files'
-import { filterRemovedAnnexObjects } from '../utils/file.js'
+import Summary from "../../models/summary"
+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 { checkDatasetWrite } from "../permissions.js"
+import { getFiles } from "../../datalad/files"
+import { filterRemovedAnnexObjects } from "../utils/file.js"
 
 // A draft must have a dataset parent
 const draftFiles = async (dataset, args, { userInfo }) => {
@@ -19,7 +19,7 @@ const draftSize = async (dataset, args, { userInfo }) => {
   const hexsha = await getDraftRevision(dataset.id)
   return Summary.findOne({ datasetId: dataset.id, id: hexsha })
     .exec()
-    .then(res => res?.toObject()?.size)
+    .then((res) => res?.toObject()?.size)
 }
 
 /**
@@ -44,15 +44,15 @@ export const revalidate = async (obj, { datasetId }, { user, userInfo }) => {
 }
 
 const draft = {
-  id: obj => obj.id,
+  id: (obj) => obj.id,
   files: draftFiles,
   size: draftSize,
   summary,
   issues,
-  modified: obj => obj.modified,
+  modified: (obj) => obj.modified,
   description,
   readme,
-  head: obj => obj.revision,
+  head: (obj) => obj.revision,
 }
 
 export default draft

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

@@ -1,5 +1,5 @@
-import BadAnnexObject from '../../models/badAnnexObject'
-import { checkAdmin } from '../permissions'
+import BadAnnexObject from "../../models/badAnnexObject"
+import { checkAdmin } from "../permissions"
 
 export const flaggedFiles = async (
   obj,
@@ -8,6 +8,6 @@ export const flaggedFiles = async (
 ) => {
   await checkAdmin(user, userInfo)
   return BadAnnexObject.find({ flagged, removed: deleted })
-    .populate('flagger')
-    .populate('remover')
+    .populate("flagger")
+    .populate("remover")
 }

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

@@ -1,4 +1,4 @@
-import Subscription from '../../models/subscription'
+import Subscription from "../../models/subscription"
 
 export const followDataset = async (obj, { datasetId }, { user }) => {
   const following = await Subscription.findOne({

package/src/graphql/resolvers/git.ts

@@ -1,6 +1,6 @@
-import { checkDatasetWrite } from '../permissions.js'
-import { generateRepoToken } from '../../libs/authentication/jwt'
-import { getDatasetEndpoint } from '../../libs/datalad-service.js'
+import { checkDatasetWrite } from "../permissions.js"
+import { generateRepoToken } from "../../libs/authentication/jwt"
+import { getDatasetEndpoint } from "../../libs/datalad-service.js"
 
 /**
  * Generate a short lived token for git operations

package/src/graphql/resolvers/history.ts

@@ -0,0 +1,13 @@
+import { getDatasetWorker } from "../../libs/datalad-service"
+
+export const history = async (obj) => {
+  const datasetId = obj.id
+  const historyUrl = `http://${
+    getDatasetWorker(
+      datasetId,
+    )
+  }/datasets/${datasetId}/history`
+  const resp = await fetch(historyUrl)
+  const { log } = await resp.json()
+  return log
+}

package/src/graphql/resolvers/importRemoteDataset.ts

@@ -1,9 +1,9 @@
-import IngestDataset from '../../models/ingestDataset'
-import { checkDatasetWrite } from '../permissions.js'
-import { getDatasetWorker } from '../../libs/datalad-service'
-import { generateDataladCookie } from '../../libs/authentication/jwt'
-import notifications from '../../libs/notifications'
-import config from '../../config'
+import IngestDataset from "../../models/ingestDataset"
+import { checkDatasetWrite } from "../permissions.js"
+import { getDatasetWorker } from "../../libs/datalad-service"
+import { generateDataladCookie } from "../../libs/authentication/jwt"
+import notifications from "../../libs/notifications"
+import config from "../../config"
 
 /**
  * Test if a URL is allowed to be imported
@@ -17,10 +17,10 @@ export function allowedImportUrl(raw: string): boolean {
   } catch (_) {
     return false
   }
-  if (url.hostname === 'brainlife.io') {
+  if (url.hostname === "brainlife.io") {
     return true
   } else if (
-    url.hostname === 'openneuro-test-import-bucket.s3.us-west-2.amazonaws.com'
+    url.hostname === "openneuro-test-import-bucket.s3.us-west-2.amazonaws.com"
   ) {
     return true
   } else {
@@ -46,11 +46,12 @@ export async function importRemoteDataset(
     await ingest.save()
     const importId = ingest._id.toString()
     const worker = getDatasetWorker(datasetId)
-    const importUrl = `http://${worker}/datasets/${datasetId}/import/${importId}`
+    const importUrl =
+      `http://${worker}/datasets/${datasetId}/import/${importId}`
     await fetch(importUrl, {
-      method: 'POST',
+      method: "POST",
       headers: {
-        'Content-Type': 'application/json',
+        "Content-Type": "application/json",
         Cookie: generateDataladCookie(config)(userInfo),
       },
       body: JSON.stringify({ url }),

package/src/graphql/resolvers/index.ts

@@ -0,0 +1,25 @@
+import { GraphQLDate, GraphQLDateTime, GraphQLTime } from "graphql-iso-date"
+import GraphQLBigInt from "graphql-bigint"
+import Query from "./query.js"
+import Mutation from "./mutation.js"
+import Dataset from "./dataset.js"
+import Draft from "./draft.js"
+import Snapshot from "./snapshots.js"
+import User from "./user.js"
+import Comment from "./comment.js"
+
+export default {
+  // Scalars
+  Date: GraphQLDate,
+  Time: GraphQLTime,
+  DateTime: GraphQLDateTime,
+  BigInt: GraphQLBigInt,
+  // Complex types
+  Query,
+  Mutation,
+  User,
+  Dataset,
+  Draft,
+  Snapshot,
+  Comment,
+}

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

@@ -1,6 +1,6 @@
-import Issue from '../../models/issue'
-import { datasetType } from './datasetType'
-import { revalidate } from './validation.js'
+import Issue from "../../models/issue"
+import { datasetType } from "./datasetType"
+import { revalidate } from "./validation.js"
 
 /**
  * Issues resolver
@@ -11,12 +11,12 @@ export const issues = async (dataset, _, { userInfo }) => {
     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()
-    .then(data => {
+    .then((data) => {
       if (!data && userInfo) {
         // If no results were found, acquire a lock and run validation
         revalidate(
@@ -32,17 +32,17 @@ export const issues = async (dataset, _, { userInfo }) => {
 /**
  * Snapshot issues resolver
  */
-export const snapshotIssues = async snapshot => {
-  const datasetId = snapshot.id.split(':')[0]
+export const snapshotIssues = async (snapshot) => {
+  const datasetId = snapshot.id.split(":")[0]
   return Issue.findOne({
     id: snapshot.hexsha,
     datasetId,
     // Match if we have no validatorMetadata or the correct 'legacy' / 'schema' value if we do
     $or: [
-      { 'validatorMetadata.validator': await datasetType(snapshot) },
+      { "validatorMetadata.validator": await datasetType(snapshot) },
       { validatorMetadata: { $exists: false } },
     ],
   })
     .exec()
-    .then(data => (data ? data.issues : null))
+    .then((data) => (data ? data.issues : null))
 }

package/src/graphql/resolvers/metadata.ts

@@ -1,9 +1,9 @@
-import Snapshot from '../../models/snapshot'
-import { LeanDocument } from 'mongoose'
-import DatasetModel from '../../models/dataset'
-import MetadataModel, { MetadataDocument } from '../../models/metadata'
-import { latestSnapshot } from './snapshots'
-import { permissions } from './permissions'
+import Snapshot from "../../models/snapshot"
+import { LeanDocument } from "mongoose"
+import DatasetModel from "../../models/dataset"
+import MetadataModel, { MetadataDocument } from "../../models/metadata"
+import { latestSnapshot } from "./snapshots"
+import { permissions } from "./permissions"
 
 /**
  * Summary resolver
@@ -28,7 +28,7 @@ export const metadata = async (
   const adminUsers = []
   const { userPermissions } = await permissions(dataset)
   for (const user of userPermissions) {
-    if (user.level === 'admin') {
+    if (user.level === "admin") {
       const userObj = await user.user
       adminUsers.push(userObj.name)
     }
@@ -50,7 +50,7 @@ export const metadata = async (
     adminUsers,
     firstSnapshotCreatedAt,
     latestSnapshotCreatedAt: snapshot.created,
-    ages: summary?.subjectMetadata?.map(s => s.age as number),
+    ages: summary?.subjectMetadata?.map((s) => s.age as number),
     modalities: summary?.modalities || [],
     dataProcessed: summary?.dataProcessed || null,
   }

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

@@ -5,41 +5,41 @@ import {
   createDataset,
   deleteDataset,
   deleteFiles,
-  removeAnnexObject,
   flagAnnexObject,
-  updatePublic,
+  removeAnnexObject,
   trackAnalytics,
-} from './dataset.js'
-import { updateRef } from './draft.js'
+  updatePublic,
+} from "./dataset.js"
+import { updateRef } from "./draft.js"
 import {
   createSnapshot,
   deleteSnapshot,
   deprecateSnapshot,
   undoDeprecateSnapshot,
-} from './snapshots.js'
-import { removeUser, setAdmin, setBlocked } from './user.js'
-import { updateSummary } from './summary'
-import { revalidate, updateValidation } from './validation.js'
-import { updatePermissions, removePermissions } from './permissions'
-import { followDataset } from './follow.js'
-import { starDataset } from './stars.js'
-import { publishDataset } from './publish.js'
-import { updateDescription, updateDescriptionList } from './description.js'
-import { updateReadme } from './readme.js'
-import { addComment, editComment, deleteComment } from './comment.js'
-import { subscribeToNewsletter } from './newsletter'
-import { addMetadata } from './metadata'
-import { prepareUpload, finishUpload } from './upload.js'
-import { prepareRepoAccess } from './git'
-import { cacheClear } from './cache'
-import { reexportRemotes } from './reexporter'
-import { resetDraft } from './reset'
-import { createReviewer, deleteReviewer } from './reviewer'
-import { createRelation, deleteRelation } from './relation'
+} from "./snapshots.js"
+import { removeUser, setAdmin, setBlocked } from "./user.js"
+import { updateSummary } from "./summary"
+import { revalidate, updateValidation } from "./validation.js"
+import { removePermissions, updatePermissions } from "./permissions"
+import { followDataset } from "./follow.js"
+import { starDataset } from "./stars.js"
+import { publishDataset } from "./publish.js"
+import { updateDescription, updateDescriptionList } from "./description.js"
+import { updateReadme } from "./readme.js"
+import { addComment, deleteComment, editComment } from "./comment.js"
+import { subscribeToNewsletter } from "./newsletter"
+import { addMetadata } from "./metadata"
+import { finishUpload, prepareUpload } from "./upload.js"
+import { prepareRepoAccess } from "./git"
+import { cacheClear } from "./cache"
+import { reexportRemotes } from "./reexporter"
+import { resetDraft } from "./reset"
+import { createReviewer, deleteReviewer } from "./reviewer"
+import { createRelation, deleteRelation } from "./relation"
 import {
-  importRemoteDataset,
   finishImportRemoteDataset,
-} from './importRemoteDataset'
+  importRemoteDataset,
+} from "./importRemoteDataset"
 
 const Mutation = {
   createDataset,

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

@@ -4,7 +4,7 @@
  * Adds emails to newsletter mailing list.
  */
 
-import Newsletter from '../../models/newsletter'
+import Newsletter from "../../models/newsletter"
 
 // finds or adds email to newsletter collection
 // returns true if email exists or is successfully created
@@ -13,7 +13,7 @@ export const subscribeToNewsletter = (obj, { email }) => {
   // check if email is not empty
   if (!email) return false
   return Newsletter.create({ email })
-    .then(subscriber => Boolean(subscriber))
+    .then((subscriber) => Boolean(subscriber))
     .catch(() => false)
 }